On-chip ultrafast mode-locking lasers are basic building blocks for the realization of a chip-based optical frequency comb. In this paper, an ultrafast saturable absorber made up of a graphene pad on top of a silicon waveguide is applied to implement an ultrafast pulse laser. Benefiting from the small mode area of the graphene/silicon hybrid waveguide, the saturable pulse energy is reduced by two orders of magnitude compared with the fiber. A mode-locked pulse with a duration of 542 fs and a repetition rate of 54.37 MHz is realized. Pump–probe measurement shows that the carrier relaxation process of free carrier recombination with atomic-thin graphene/silicon junctions is three orders of magnitude faster than silicon, which plays a fundamental role in pulse narrowing. The chip-scale silicon ultrafast laser lays a foundation for a new class of nonlinear devices, in which a combination with multiple functional silicon photonic circuits enables efficient nonlinear interaction at the micrometer scale and less than 1 W of power consumption.