The aim of this study was to investigate the effects of welding current and welding time on the microstructure and mechanical properties of welding joints. To this end, two dissimilar materials, austenitic stainless steel alloy SUS301L and aluminum alloy 6063-T6, were welded together via intermediate frequency resistance spot welding. A thick, two-layered intermetallic compound layer containing FeAl3 and Fe2Al5 phases was formed at the SUS301L/6063-T6 interface. As the welding current and welding time increased, the nugget diameter increased, the interfacial layer structure became coarser, the thickness of the interfacial intermetallic compound increased, and the tensile shear load of the weld joints had an increased welding tendency in stainless steel/aluminum joints. The nugget diameter reached 5.4 mm, and the maximum tensile shear load reached 1783 N at 7 kA for 200 ms of welding time. The resistance spot welded joint exhibited an interfacial fracture mode in the welded joint. The crack initiated at the interfacial intermetallic compound layer near the aluminum alloy side and spread through the interfacial layer, as well as through the aluminum alloy fusion zone near the interface.