A window management method in an electronic device and an electronic device thereof are provided. The method includes displaying, on a display, a first window; displaying, on the display with the first window, a second window as a pop-up window or a split window; displaying a handler for adjusting a size of at least one of the first window and the second window at a boundary area of the first window or the second window; and changing the displayed split window into the pop-up window or the displayed pop-up window into the split window in response to a user input to the handler.