потому что fadeIn добавляет display: block css к вашему элементу.попробуйте код ниже.
$(".edit_button").click(function(){
$('.edit_modal_overlay_maincontainer').css({opacity: 0, display: 'flex'}).animate({
opacity: 1
}, 300);
});
$(".edit_modal_header_close").click(function(e){
e.preventDefault();
$('.edit_modal_overlay_maincontainer').css('display','none');
});
body{display:flex; flex-direction:column; position:relative; font-family:Open Sans;}
*{box-sizing:border-box; margin:0; padding:0;}
a{text-decoration:none;}
table, th, td {border: 1px solid rgba(0,0,0,0.2); border-collapse: collapse;}
th, td {padding: 4px 8px;}
th { text-align: left;}
.pointer{cursor:pointer;}
.navbar_maincontainer{width:100%; height:8vh; background-color:#605CA8; display:flex; align-items:center;}
.navbar_logo_container{width:280px; height:100%; position:relative; display:flex; align-items:center; padding:0px 15px; border-right:1px solid rgba(0,0,0,0.);}
.navbar_gradient{width:100%; height:100%; position:absolute; right:0px; top:0px; background: linear-gradient(to left, rgba(52, 50, 89, 0.7), rgba(52, 50, 89, 0));}
.navbar_logo_part1{z-index:9999999999; font-family:Rubik; font-size:24px; color:#00ffa1;}
.navbar_logo_part2{font-size:23px; color:rgba(255,255,255,0.85);}
.navbar_menu_toggle{font-size:26px; color:rgba(255,255,255,1.0); margin-left:15px;}
.navbar_menu_toggle:hover{color:#2A3F54;}
.navbar_logout_container{width:auto; height:35px; display:flex; align-items:center; margin-left:auto; margin-right:30px; font-family:Open Sans;}
.navbar_logout_icon{font-size:26px; color:rgba(255,255,255,1.0); margin-left:auto; margin-right:5px;}
.navbar_logout_text{font-size:17px; color:rgba(255,255,255,1.0);}
.navbar_logout_container:hover .navbar_logout_icon{color:#2A3F54;}
.navbar_logout_container:hover .navbar_logout_text{color:#2A3F54;}
.admin_maincontainer{width:100%; height:92vh; display:flex;}
.sidebar_maincontainer{overflow-x:hidden; width:280px; height:100%; transition:all 100ms ease; display:flex; flex-direction:column; background-color:#2A3F54; box-shadow:4px 4px 4px rgba(0,0,0,0.3); align-items:center;}
.active_sidebar_maincontainer{width:0px;}
.sidebar_user_container{width:100%; height:90px; display:flex; padding:10px; margin:5px 0px;}
.sidebar_user_image{width:60px; height:60px; border-radius:50%; background-color:#01B271; display:flex;}
.sidebar_user_image_letter{margin:auto; font-size:25px; color:rgba(255,255,255,0.9); font-weight:600;}
.sidebar_user_info_container{width:auto; height:100%; display:flex; flex-direction:column; padding:5px 5px 5px 10px;}
.sidebar_user_info_name{font-size:19px; color:rgba(255,255,255,1.0); font-weight:500;}
.sidebar_user_info_role_container{width:100%; display:flex; height:25px; align-items:center;}
.sidebar_user_info_status{width:7px; height:7px; border-radius:50%; background-color:#3C763D; margin-right:5px;}
.sidebar_user_info_role{font-size:10px; color:rgba(255,255,255,0.8); font-weight:300;}
.sidebar_user_info_last_conection{font-size:10px; color:rgba(255,255,255,0.8); font-weight:300; margin-top:7px;}
.sidebar_search_container{width:90%; height:45px; display:flex; align-items:center; border-radius:11px; background-color:#3A4851; margin-top:20px; margin-bottom:15px; overflow:hidden;}
.sidebar_search_input{width:85%; height:100%; padding:10px; background-color:#3A4851; border:1px solid #3A4851; color:rgba(255,255,255,0.9); font-size:17px;}
.sidebar_search_input:focus {border-color: none;-webkit-box-shadow: none; box-shadow: none; outline: none;}
.sidebar_search_button{width:15%; height:100%; background-color:#3A4851; display:flex;}
.fa-search{font-size:20px; color:rgba(255,255,255,0.9); margin:auto;}
.sidebar_entries_container{width:100%; height:auto; overflow-x:hidden; overflow-y:auto; border-top:1px solid rgba(42,63,84,0.5);}
.sidebar_entry_container{width:100%; height:auto; display:flex; flex-direction:column; border-bottom:1px solid rgba(255,255,255,0.1);}
.sidebar_entry_container:hover{cursor:pointer;}
.sidebar_entry_link_container{width:100%; height:50px; display:flex; align-items:center; padding:10px; position:relative;}
.sidebar_entry_link_container:hover{}
.sidebar_entry_link_icon_container{width:30px; height:100%; display:flex; justify-content:center; align-items:center; margin-right:5px;}
.active_entry{background-color:#1c2a38;}
.sidebar_entry_link_icon{font-size:19px; color:rgba(255,255,255,0.9);}
.sidebar_entry_link_item{font-size:18px; color:rgba(255,255,255,0.9); font-weight:500;}
.sidebar_entry_dropdown_container{width:100%; height:auto; display:flex; flex-direction:column; display:none;}
.sidebar_entry_dropdown_item{width:100%; height:35px; display:flex; transition:all 400ms ease; align-items:center; padding:0px 20px; font-size:14px; color:rgba(255,255,2555,0.9);}
.sidebar_entry_dropdown_item:hover{background-color:#3A4851}
.fa-chevron-right{color:rgba(255,255,255,0.9); font-size:8px; margin-right:10px; transition:all 400ms ease;}
.fa-chevron-down{font-size:14px; color:rgba(255,255,255,0.9); position:absolute; top:50%; transform:translateY(-50%); right:11px;}
.body_maincontainer{width:80%; height:100%; background-color:rgba(0,0,0,0.1); padding:50px;}
.active_body_maincontainer{width:100%; }
.body_entry_container{width:100%; height:35px; display:flex; align-items:center; margin-bottom:15px;}
.body_entry_title{font-size:27px; color:rgba(0,0,0,0.8);; font-weight:600; margin-right:10px;}
.body_entry_new_container{border-radius:7px; display:flex; align-items:center; background-color:#337AB7; padding:4px 8px;}
.body_entry_new_plus{color:white; font-size:12px; margin-right:5px;}
.body_entry_new_text{font-size:16px; color:white; font-weight:500;}
.body_table_maincontiner{width:100%; font-size:12px; background-color:white;}
.body_table_options_container{display:flex;}
.body_table_option_edit_container{width:25px; height:25px; border-radius:5px; display:flex; background-color:#5BC0DE; margin-right:10px;}
.body_table_option_delete_container{width:25px; height:25px; border-radius:5px; display:flex; background-color:#D9534F;}
.body_table_option_icon{color:white; font-size:15px; margin:auto;}
.edit_modal_overlay_maincontainer{width:100%; height:100vh; background-color:rgba(0,0,0,0.7); position:absolute; top:0px; left:0px; display:flex; justify-content:center; align-items:center; z-index:999999999999999999999999999; transition: all 0.5s ease-in-out}
.edit_modal_container{ width:55%; height:82%; border:1px solid rgba(0,0,0,0.2); background-color:white; border-radius:20px; display:flex; flex-direction:column;}
.edit_modal_header_container{width:100%; height:13%; display:flex; align-items:center; position:relative; padding:0px 20px;}
.edit_modal_header_close{position:absolute; top:50%; transform:translateY(-50%); right:25px;}
.fa-times-circle{color:rgba(0,0,0,0.2); font-size:30px;}
.edit_modal_header_title{font-size:25px; color:rgba(0,0,0,0.8); font-weight:600;}
.edit_modal_header_line{width:94%; height:1px; position:absolute; left:50%; transform:translateX(-50%); bottom:0px; border-bottom:1px solid rgba(0,0,0,0.2);}
.edit_modal_body_container{font-family:Open Sans; width:100%; height:74%; overflow:auto; padding:10px 20px 10px 20px; display:flex; flex-direction:column;}
.edit_modal_body_options_container{width:100%; height:30px; display:flex; align-items:center; margin:10px 0px;}
.edit_modal_body_options_select_title{font-size:14px; color:rgba(0,0,0,0.9); font-weight:900; margin-right:10px;}
.edit_modal_body_options_select{width:20%; height:30px; border-radius:5px; border:1px solid rgba(0,0,0,0.2);}
.edit_modal_body_options_select_options{color:rgb(0,0,0,0.8);}
.edit_modal_options_image_upload{display:flex; align-items:center; width:auto; height:35px; border: 2px solid rgba(0,0,0,0.9); margin-left:auto; border-radius: 5px; padding: 5px 7px; background-color: rgba(0,0,0,0.1); color:rgba(0,0,0,0.9); font-weight:900; font-size:14px;}
label.edit_modal_options_image_upload input[type="file"] {position:absolute; top: -1000px;}
.fa-picture-o{color:rgba(0,0,0,0.9); font-size:20px; margin-right:5px;}
.edit_modal_input{font-family:Open Sans; margin:10px 0px; font-size:13px; width:50%; height:30px; border-radius:5px; padding:7px 7px; box-shadow:none; border:1px solid rgba(0,0,0,0.2);}
.edit_modal_input_textarea{font-family:Open Sans; margin:10px 0px; width:100%; height:300px; border-radius:5px; padding:7px; box-shadow:none; border:1px solid rgba(0,0,0,0.2);}
.edit_modal_footer_container{width:100%; height:13%; position:relative; display:flex; align-items:center; padding:20px;}
.edit_modal_footer_line{width:94%; height:1px; position:absolute; left:50%; transform:translateX(-50%); top:0px; border-bottom:1px solid rgba(0,0,0,0.2);}
.edit_modal_reset_add_button{margin:0px 5px; margin-left:auto; font-size:15px; padding:0px 10px; height:30px; background-color:#67C4DD; border-radius:5px; color:white; display:flex; justify-content:center; align-items:center;}
.edit_modal_footer_reset_button{margin:0px 5px; font-size:15px; padding:0px 10px; height:30px; background-color:#D9534F; border-radius:5px; color:white; display:flex; justify-content:center; align-items:center;}
.hide{display:none;}
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<div class="edit_modal_overlay_maincontainer hide">
<form class="edit_modal_container">
<div class="edit_modal_header_container">
<a class="edit_modal_header_close" href=""><i class="fa fa-times-circle"></i></a>
<h2 class="edit_modal_header_title">Nuevo post</h2>
<div class="edit_modal_header_line"></div>
</div>
<div class="edit_modal_body_container">
<div class="edit_modal_body_options_container" style="">
<span class="edit_modal_body_options_select_title" style=" ">Categorias</span>
<select class="edit_modal_body_options_select" style="">
<option class="edit_modal_body_options_select_options" value="Noticias">Noticias</option>
<option class="edit_modal_body_options_select_options" value="saab">Clases</option>
<option class="edit_modal_body_options_select_options" value="mercedes">Evento</option>
<option class="edit_modal_body_options_select_options" value="audi">Blog</option>
</select>
<label class="edit_modal_options_image_upload pointer">
<input type="file" required/>
<i class="fa fa-picture-o"></i>
<span>Imagen</span>
</label>
</div>
<input class="edit_modal_input" style="" type="text" placeholder="Titulo del post">
<input class="edit_modal_input" style="" type="text" placeholder="Resumen del post">
<input class="edit_modal_input" style="" type="text" placeholder="Descripción de la imagen">
<textarea class="edit_modal_input_textarea" style="" type="textarea" placeholder="Contenido del post"></textarea>
</div>
<div class="edit_modal_footer_container" style="">
<div class="edit_modal_footer_line" style=""></div>
<a class="edit_modal_reset_add_button" href="" title="" style="">Añadir</a>
<a class="edit_modal_footer_reset_button" href="" title="" style="">Reset</a>
</div>
</form>
</div>
<div class="navbar_maincontainer">
<div class="navbar_logo_container">
<h1 class="navbar_logo_part1">Gab<span class="navbar_logo_part2">admin</span></h1>
<div class="navbar_gradient"></div>
</div>
<i class="navbar_menu_toggle fa fa-bars pointer"></i>
<a class=" navbar_logout_container pointer" href="{{ route('logout') }}" title="Salir del administrador">
<i class="fa fa-sign-out navbar_logout_icon"></i>
<span class="navbar_logout_text">Salir</span>
</a>
</div>
<div class="admin_maincontainer">
<div class="sidebar_maincontainer">
<div class="sidebar_user_container">
<div class="sidebar_user_image">
<span class="sidebar_user_image_letter">G</span>
</div>
<div class="sidebar_user_info_container">
<span class="sidebar_user_info_name">¡Hola Gabriel!</span>
<span class="sidebar_user_info_last_conection">Ult. conexión: 04/05/2018</span>
<div class="sidebar_user_info_role_container">
<div class="sidebar_user_info_status"></div>
<span class="sidebar_user_info_role">Super Admin</span>
</div>
</div>
</div>
<div class="sidebar_search_container">
<input class="sidebar_search_input" type="text" placeholder="Buscar...">
<a class="sidebar_search_button" href=""><i class="fa fa-search"></i></a>
</div>
<div class="sidebar_entries_container">
<div class="sidebar_entry_container">
<div class="sidebar_entry_link_container">
<div class="sidebar_entry_link_icon_container">
<i class="fa fa-user sidebar_entry_link_icon"></i>
</div>
<span class="sidebar_entry_link_item">Usuarios</span>
</div>
<!--<div class="sidebar_entry_dropdown_container">
<div class="sidebar_entry_dropdown_item"><i class="fa fa-chevron-right"></i> Admin</div>
<div class="sidebar_entry_dropdown_item"><i class="fa fa-chevron-right"></i> Clientes</div>
</div>-->
</div>
<div class="sidebar_entry_container">
<div class="sidebar_entry_link_container">
<div class="sidebar_entry_link_icon_container">
<i class="fa fa-newspaper-o sidebar_entry_link_icon"></i>
</div>
<span class="sidebar_entry_link_item">Posts</span>
</div>
<!--<div class="sidebar_entry_dropdown_container">
<div class="sidebar_entry_dropdown_item"><i class="fa fa-chevron-right"></i> Admin</div>
<div class="sidebar_entry_dropdown_item"><i class="fa fa-chevron-right"></i> Admin</div>
<div class="sidebar_entry_dropdown_item"><i class="fa fa-chevron-right"></i> Admin</div>
</div>-->
</div>
<div class="sidebar_entry_container">
<div class="sidebar_entry_link_container">
<div class="sidebar_entry_link_icon_container">
<i class="fa fa-tag sidebar_entry_link_icon"></i>
</div>
<span class="sidebar_entry_link_item">Tags</span>
</div>
<!--<div class="sidebar_entry_dropdown_container">
<div class="sidebar_entry_dropdown_item"><i class="fa fa-chevron-right"></i> Admin</div>
<div class="sidebar_entry_dropdown_item"><i class="fa fa-chevron-right"></i> Admin</div>
<div class="sidebar_entry_dropdown_item"><i class="fa fa-chevron-right"></i> Admin</div>
</div>-->
</div>
</div>
</div>
<div class="body_maincontainer">
<div class="body_entry_container">
<span class="body_entry_title">Post</span>
<a class="body_entry_new_container pointer" title="Crear nuevo">
<i class="fa fa-plus body_entry_new_plus"></i>
<span class="body_entry_new_text">Nuevo</span>
</a>
</div>
<table class="body_table_maincontiner">
<tr>
<th width="10%">Firstname</th>
<th width="10%">Lastname</th>
<th width="10%">Age</th>
<th width="1%">Acción</th>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container">
<a class="body_table_option_edit_container pointer edit_button" title="Editar">
<i class="fa fa-pencil body_table_option_icon"></i>
</a>
<a class="body_table_option_delete_container pointer" title="Borrar">
<i class="fa fa-trash-o body_table_option_icon"></i>
</a>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container">
<a class="body_table_option_edit_container pointer edit_button" title="Editar">
<i class="fa fa-pencil body_table_option_icon"></i>
</a>
<a class="body_table_option_delete_container pointer" title="Borrar">
<i class="fa fa-trash-o body_table_option_icon"></i>
</a>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container">
<a class="body_table_option_edit_container pointer edit_button" title="Editar">
<i class="fa fa-pencil body_table_option_icon"></i>
</a>
<a class="body_table_option_delete_container pointer delete_button" title="Borrar">
<i class="fa fa-trash-o body_table_option_icon"></i>
</a>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container">
<a class="body_table_option_edit_container pointer edit_button" title="Editar">
<i class="fa fa-pencil body_table_option_icon"></i>
</a>
<a class="body_table_option_delete_container pointer" title="Borrar">
<i class="fa fa-trash-o body_table_option_icon"></i>
</a>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container" style="">
<a class="body_table_option_edit_container pointer edit_button" title="Editar">
<i class="fa fa-pencil body_table_option_icon"></i>
</a>
<a class="body_table_option_delete_container pointer" title="Borrar">
<i class="fa fa-trash-o body_table_option_icon"></i>
</a>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container">
<a class="body_table_option_edit_container pointer edit_button" title="Editar">
<i class="fa fa-pencil body_table_option_icon"></i>
</a>
<a class="body_table_option_delete_container pointer" title="Borrar">
<i class="fa fa-trash-o body_table_option_icon"></i>
</a>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container">
<a class="body_table_option_edit_container pointer edit_button" title="Editar">
<i class="fa fa-pencil body_table_option_icon"></i>
</a>
<a class="body_table_option_delete_container pointer" title="Borrar">
<i class="fa fa-trash-o body_table_option_icon"></i>
</a>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container">
<a class="body_table_option_edit_container pointer edit_button" title="Editar">
<i class="fa fa-pencil body_table_option_icon"></i>
</a>
<a class="body_table_option_delete_container pointer" title="Borrar">
<i class="fa fa-trash-o body_table_option_icon"></i>
</a>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container">
<span class="body_table_option_edit_container pointer">
<i class="fa fa-pencil body_table_option_icon"></i>
</span>
<span class="body_table_option_delete_container pointer">
<i class="fa fa-trash-o body_table_option_icon"></i>
</span>
</td>
</tr>
<tr>
<td>Jill</td>
<td>Smith</td>
<td>50</td>
<td class="body_table_options_container" style="">
<span class="body_table_option_edit_container pointer" style="">
<i class="fa fa-pencil body_table_option_icon" style=""></i>
</span>
<span class="body_table_option_delete_container pointer" style="">
<i class="fa fa-trash-o body_table_option_icon" style=""></i>
</span>
</td>
</tr>
</table>
</div>
</div>