High-quality joining of dissimilar alloys between Fe-36Ni alloy and 304L stainless steel is essential in the manufacturing of LNG tanker. In this study, lap joints of Fe-36Ni and 304L dissimilar alloys were fabricated by a pulsed gas tungsten arc welding (P-GTAW) process. The effects of low-frequency pulse on the appearance, microstructure and mechanical properties of the Fe-36Ni/304L lap joints was investigated. With the increase of frequency, the feature sizes of α (the transition angle of the upper surface of Fe-36Ni to the surface of the weld bead) and R (shortest distance between weld root and weld surface) exhibited downtrend and uptrend, respectively, while La (the maximum weld width of lower sheet) and P (the maximum weld penetration of lower sheet) changed in a smaller range. Fusion zone (FZ) is mainly composed of γ phase and M23C6 during solidification, and M23C6 particles are distributed on the grain boundaries of the cells, which reduced the mechanical properties of joint. The average hardness between 110 HV1 and 136 HV1 is lower than that of the base metals. Fractures of all joints located at the Fe-36Ni side near the weld, and a dimple fracture in all samples indicated a ductile fracture. This study found that the heat input values remain 198.86 J mm−1 and increased pulse frequency can improve the maximum tensile force. The average maximum tensile force of the lap weld is 11.95 kN when pulsed frequency is 15 Hz.