Fatigue analysis of swept friction stir clinch (Swept-FSC) joints between 6061-T6 aluminum (Al) and S45C steel (Fe) sheets was conducted through experimental approaches. Before fatigue tests, a parametric study for the probe geometry of FSC tools was conducted in order to eliminate the hook structure inside the joint and improve the mechanical performance of the joint. Then a series of quasi-static and fatigue tests for Al/Fe Swept-FSC joints in lap-shear (LP) and cross-tension (CT) specimens were conducted. The fatigue data were recorded. The fatigue behavior of Al/Fe Swept-FSC joints in LP and CT specimens were examined through optical and scanning electron microscopes. Experimental results indicated that LP specimens have two failure modes, while CT specimens have only one failure mode. The dominant fatigue crack of each failure mode was identified.