Passive mode-locking in quantum cascade lasers (QCLs) remains one of the huge challenges because of the fast relaxation time of the excited carriers which is typically in the range of sub-picoseconds. The use of conventional techniques such as the semiconductor saturable absorber mirror is inefficient because the spatial hole burning effect dominates the carrier dynamics. To overcome this effect, longitudinal transition structures with relaxation time around \(50 \mathrm{ps}\) were proposed. However, mode-locking is assured with an external modulation at a cavity roundtrip frequency. In this paper, we demonstrate that a single-layer graphene used as a saturable absorber permits to generate stable pulses in such structures. The graphene is integrated with a highly reflective mirror to increase the internal electric field and achieve the saturation intensity. The dynamic of the QCL is modeled with Maxwell-Bloch equations and the graphene layer with Maxwell-Ampere equation. This system of equations is solved using the one-dimensional Finite-Difference Time-Domain (FDTD) method. To model the graphene layer of \(0.33 \mathrm{nm}\) thickness, a specific sub-cell is implemented using Maloney method. Simulation results show a generation of isolated pulses with a peak electric field of \(80 \mathrm{\frac{MV}{m}}\) and a duration of \(51 \mathrm{fs}\). The mode-locking remains stable for the QCL with a vertical transition having a relaxation time below \(5 \mathrm{ps}\).