A proposed bilevel optimization process determines the depth of a dipped vertical alignment between rail transit stations as well as the cruising speed for each direction. This model also considers how regenerative braking may affect vertical alignment decisions. The optimized depth and directional cruising speeds were jointly obtained in a numerical example. A sensitivity analysis showed that regenerative braking reduced the total cost but did not significantly change the optimized depth of the dipped vertical alignment. The developed model is more realistic and useful than previous ones because it allows unequal station elevations, jointly optimizes decision variables, and considers regenerative braking.