Заимствовано из MSDN ( текст ссылки ):
using System.Runtime.InteropServices;
...
[DllImport("user32.dll")]
public static extern IntPtr FindWindow(string lpClassName,string lpWindowName);
[DllImport("user32.dll")]
static extern bool ShowWindow(IntPtr hWnd, int nCmdShow);
...
//Sometimes System.Windows.Forms.Application.ExecutablePath works for the caption depending on the system you are running under.
IntPtr hWnd = FindWindow(null, "Your console windows caption"); //put your console window caption here
if(hWnd != IntPtr.Zero)
{
//Hide the window
ShowWindow(hWnd, 0); // 0 = SW_HIDE
}
if(hWnd != IntPtr.Zero)
{
//Show window again
ShowWindow(hWnd, 1); //1 = SW_SHOWNORMA
}