An apparatus and method for preventing a shut down in limphome driving are provided. The apparatus includes an engine clutch and a hybrid control unit (HCU) that is configured to operate a vehicle by dualizing a driving of the vehicle into a normal driving control and a limphome driving control. When the driving of the vehicle is in the limphome driving control, the HCU is configured to reduce a vehicle speed and perform a control right shift based on a status of the engine clutch. In addition, an engine control unit (ECU) is configured to compare a current engine revolution per minute (RPM) with a targeted engine RPM based on the control right shift to operate the engine to adjust the engine RPM to reach the targeted engine RPM.