The hydrodynamic benefits of fixed and flapping pectoral fins were explored using the penalty immersed boundary method. A self-propelled flexible plate was realized in the present study, where a clamped leading edge of the flexible plate was forced into a prescribed harmonic oscillation in the spanwise direction but was free to move in the horizontal direction. The body and pectoral fins of a fish were modeled using a flexible plate and two rigid/flexible plates. Simulations without the pectoral fins were also performed for comparison. The pressure distributions and vortical structures around the plate were visualized to characterize the hydrodynamic roles of the pectoral fins. The vortices generated by the pectoral fins increase the pressure difference between the upper and lower sides of the plate, resulting in an enhancement of both the cruising speed (10.5%) and thrust. The horizontally flapping pectoral fins with low flapping frequency enhance the propulsive efficiency rather than the fixed pectoral fins. The flexible flapping fins enhance the cruising speed rather than the rigid flapping fins. In addition, the presence of one flapping fin on one side of the flexible plate induces asymmetrical heaving of the flexible plate and increases the lateral forces, which might help fish achieve turning and maintain balance in perturbed flows.