An HVAC controller may be programmed using a mobile device having a touch screen display, a wireless port and a controller that is in operative communication with the touch screen display and the wireless port. The controller may establish communication with and download an application program code from the remote download server. The controller may establish a direct wireless connection between the wireless port of the mobile device and the wireless interface of the HVAC controller and execute the application program code, which provides one or more configuration screens on the touch screen display of the mobile device to enable the user to configure the HVAC controller via one or more configuration parameters, and then upload the one or more configuration parameters to the HVAC controller via the direct wireless connection between the wireless port of the mobile device and the wireless interface of the HVAC controller.