A remote initialization system and method for a vehicle system receive trip data for an upcoming trip at an off-board device. Using the off-board device, the trip data is communicated to the different back-office systems, and one or more of mandatory directives or software configuration requirements are received at the off-board device from the different back-office systems. An initialization data set that includes at least some of the trip data and at least some of the one or more of the mandatory directives or the software configuration requirements is communicated from the off-board device to an onboard controller of the vehicle system. The initialization data set is configured to be used by the onboard controller to control movement of the vehicle system in the different sets of the routes.