Schedule coordination is a proven strategy to improve the connectivity and service quality for bus networks, whereas current research mostly optimizes schedule design using the a priori knowledge of users’ routings and ignores the behavioural reactions to coordination status. This study proposes a novel stochastic bus schedule coordination design with demand assignment and passenger rerouting in case of transfer failure. To this end, we develop a bi-level programming model in which the schedule design (headways and slack times) and passenger route choice are determined simultaneously via two travel strategies: non-adaptive and adaptive routings. In the second strategy, transfer passengers would modify their paths in case of missed connection. In this way, the expected network flow distribution is dependent on both the transfer reliability and network structure. The upper-level problem is formulated as a mixed integer non-linear program with the objective of minimizing the total system cost, including both operation cost and user cost, while the lower-level problem is route choice (pre-trip and on-trip) model for timed-transfer service. A more generalized inter-ratio headways scenario is also taken into account. A heuristic algorithm and the method of successive averages are comprehensively applied for solving the bi-level model. Results show that when the rerouting behaviour is considered, more cost-effective schedule coordination scheme with less slack times can be achieved, and ignoring such effect would underestimate the efficacy of schedule coordination scheme.