Provided is a transit management server, system and method for managing transit fares for a transportation system. The method includes selecting, in a transit management server, at least one fare module according to a transit fare policy, the at least one fare module corresponding to a prescribed category of fare and configured to determine a fare based on the prescribed category, setting, in the transit management server, at least one parameter in the selected fare module, and transmitting, from the transit management server to at least one terminal communicatively coupled to the transit management server, the set parameter to update a corresponding fare module in the at least one terminal according to the transit fare policy.