The focus of this chapter is transit fare optimization problem in transit networks with one operator as well as when multiple operators are present. A bi-level programming approach is adopted to determine the optimal fare structure of the transit network where the passengers' route choice behavior is taken into account using a stochastic user equilibrium (SUE) transit assignment model. The optimal fare problem is first investigated for the case of a transit system with one operator and subsequently extend it to the deregulated transit market with multiple operators. The capacity restraint SUE transit assignment models with elastic demand and elastic line frequency can then be incorporated respectively.