During the COVID-19 outbreak, serious concerns were raised over the risk of spreading the infection on public transportation systems. As the pandemic recedes it will be important to determine optimal timetable design to minimize the risk of new infections as systems resume full service. In this study, we developed an integrated optimization model for service line reopening plans and timetable design. Our model combines a space-time passenger network flow problem and compartmental epidemiological models for each vehicle and platform in the transit system. The algorithm can help policy makers to design schedules under COVID-19 more efficiently. The report develops an optimized timetable for the Bay Area Rapid Transit system. We found that if passengers choose other mode of transportation when closing part of the system or decreasing the frequency of service can prevent the spread of infections, otherwise, if passengers choose to use the closest open station, closings will lead to longer waiting times, higher passenger density and greater infection risk. We found that the goal of stopping the spread of infection could be achieved by minimizing the total delay when infections were similar in different districts across the service area. Where infection rates are different in different districts, minimizing the risk of exposure can be achieved by minimizing weighted travel time where higher weights are applied to areas where the infection rate is highest.