Recently, inspired by the flippers of humpback whales, researchers have been widely studying leading-edge tubercles for use as passive flow control devices. In this research, we numerically investigated the effects of leading-edge tubercles on a three-dimensional flapping foil coupled with rolling and pitching motions. Appropriate spanwise flexibility is considered to mimic the real flapping motion of humpback whales, and the profile of the angle of attack was analyzed in a representative section under the effects of spanwise flexibility. The motion of flexible foils was decomposed into rigid motion and flexible deflection by using the sliding mesh and dynamic mesh methods, respectively. Then, the hydrodynamic performance of the flexible flapping foils was estimated by solving the unsteady Reynolds Averaged Navier–Stokes equations. The effects of the shape and kinematic parameters on thrust, power consumption, and propulsive efficiency were studied and the mechanism behind these effects was investigated. A maximum efficiency loss of 19.4% was observed for the sharpest tubercle shape. Although the hydrodynamic advantages of leading-edge tubercles were not observed in the present study, the tendency of flow separation over peaking sections was suppressed under low angles of attacks. The results suggest that leading-edge tubercles are more suitable for foils with steady or quasi-steady motions, such as propellers or turbines.