The microstructural characteristics and mechanical properties of friction stir lap welding (FSLW) of thin Al-clad Al (1.5 mm) and ultra-thin Al-clad mild steel (0.7 mm) sheets are experimentally investigated. Optical microscopic observation confirms that the FSLW joints are successfully fabricated without noticeable joining defects, such as cracks and hooks. The material flow is correlated with the silicon (Si) element distribution in the stir zone (SZ). The distribution of Si indicates that material flow is asymmetrical between the advancing side (AS) and the retreating side (RS) of the SZ. The tensile test result shows that all the FSLW joints fracture from the Al-clad Al side of the joints. During the fatigue tests, two different crack propagation modes (vertical crack in the Al-clad Al loading side; horizontal crack in the Al-clad mild steel loading side) are observed simultaneously due to the combined effect of the asymmetric geometry of the FSLW joint and the different loading configurations. The results of fatigue tests suggest that the asymmetric microstructure of the joint retards the propagation of a vertical crack in the Al-clad Al loading side for the RS-loaded FSLW joint. As a result, the fatigue life of the RS-loaded FSLW joint becomes clearly higher than that of the AS-loaded FSLW joint.