Multi-material fabrication such as joining of steel and aluminium has become prominent now-a-days in automotive industries. Friction stir welding being a novel solid state welding process, has already established good joint strength between steel and aluminium; but fatigue strength of such dissimilar joint has not yet been explored. In the present study, the friction stir lap welding was performed at each rotation speed of 500, 1000, 1500 for two different travel speed i.e. 50 and 100 mm min−1 at a constant probe depth of 2.5 mm. Among the six different joints, joint strength achieved of maximum (5 kN) and minimum (2 kN) under two parameter combination i.e. 1000 rpm 50 mm min−1 and 500 rpm 100 mm min−1 respectively, have been exclusively characterized by high cycle fatigue at R ratio 0.1. Furthermore, R ratio has been varied from +0.5, +0.3 to −0.5, −0.3 at a particular load amplitude which shows the endurance limit (106 cycles) for both combination of parameters. The experimental results show that fatigue strength at 106 cycles for both the FS welded lap joint is about 20 % of their respective failure load. Thus better fatigue strength is associated with the lap joint performed with the joint of maximum load. The fatigue behaviour of two FS joints has been correlated with the thickness of intermetallic compound and accumulation of dislocations observed by TEM.