This paper deals with the transit passenger origin-destination (O-D) estimation problem by using updated passenger counts in congested transit networks and outdated prior O-D matrix. A bilevel programming approach is extended for the transit passenger O-D updating problem where the upper-level problem seeks to minimize the sum of error measurements in passenger counts and O-D matrices, while the lower level is the stochastic user equilibrium assignment problem for congested transit networks. The transit assignment framework is based on a frequency-adaptive transit network model in this paper, which can help determine transit line frequencies and the network flow pattern simultaneously in congested transit networks. A heuristic solution algorithm is adapted for solving the transit passenger O-D estimation problem. Finally, a numerical example is used to illustrate the applications of the proposed model and solution algorithm.