Perimeter control involves monitoring network-wide traffic and regulating traffic inflow to alleviate hypercongestion. Implementation of transit priority with perimeter control measures, which allow transit into a controlled area without queuing at the perimeter boundary, is an effective strategy in bimodal transportation systems. However, travelers’ behavior changes in response to perimeter control strategies, such as shifts in their departure times and transportation modes, have not been fully investigated. Therefore, important questions remain, such as the use of transit during perimeter control with transit priority. This paper examines the travelers’ behavior changes in response to perimeter control with transit priority in a mixed bimodal transportation system with cars and flexible route transit (FRT) vehicles. We model departure time and transportation mode choices in such a transportation system with hypercongestion and discomfort in FRT (called the mixed bimodal bathtub model). Initially, we investigate the properties of dynamic user equilibrium without perimeter control. Then, we study the equilibrium patterns during perimeter control with transit priority. Unlike existing works, we find that the number of FRT passengers decreases with time toward the desired arrival time and that FRT may not be used around the peak of rush hour. Furthermore, transit priority may not be sufficient to promote the use of FRT, and additional incentive such as subsidy for lower fares may be required to encourage FRT use during perimeter control. Finally, we show that operating many FRT vehicles does not always decrease the equilibrium cost, even under perimeter control with transit priority.