A bilevel model is presented to optimize the fare structure for transit networks with elastic demand under the assumption of fixed transit service frequency. It is known that the transit fare structure has significant effects on passengers' demand and route choice behavior. The transit operator therefore should predict passengers' response to changing fare charges. A bilevel programming method is developed to determine the optimal fare structure for the transit operator while taking passengers' response into account. The upper-level problem seeks to maximize the operator's revenue, whereas the lower-level problem is a stochastic user equilibrium transit assignment model with capacity constraints. A heuristic solution algorithm based on sensitivity analysis is proposed. Finally, a numerical example is given together with some useful discussion.