A remote programming system for engine control units of vehicles operates by coupling an onboard diagnostic interface device with an engine control unit of a vehicle, communicatively linking the interface device with a hand held device, communicatively linking the hand held device with a back end programming machine that is remotely located from the vehicle, communicating identifying information about the vehicle to the programming machine via the interface device, the hand held device, and the communication network(s), determining an action and programming information needed to program the engine control unit of the vehicle to accept a replacement key, sending the action and programming information from the programming machine to the hand held device via the communication network(s), and programming the engine control unit of the vehicle to accept the replacement key to activate the vehicle using or responsive to use of the action and programming information.