Materials for lightweight vehicle structures play an increasingly important role in both economic and environmental terms; high-strength steels and aluminum alloys are suitable for this role. Resistance spot welding (RSW) and conventional clinching (CCL) methods can be used for joining vehicle bodies and can also be applied for aluminum/steel hybrid joints. Whereas vehicle structures are subjected to cyclic loading, damages can occur due to high-cycle fatigue (HCF) during long-term operation. Systematic HCF test results are rarely found in the literature, while HCF loading basically determines the lifetime of the hybrid joints. The base materials 5754-H22, 6082-T6, and DP600 were used for similar and hybrid RSW and CCL joints, and HCF tests were performed. The number of cycles-to-failure values and failure modes were studied and analyzed. Based on the experimental results, HCF design curves belonging to a 50% failure probability were calculated for all cases, and the curves were compared. Clear relationships were found between the failure modes and fatigue cycle numbers for both joining methods. Considering the steel/steel joints as a base, the load-bearing capacity of the hybrid joints is lower (48.7% and 73.0% for RSW, 35.0% and 38.7% for CCL) and it is even lower for the aluminum/aluminum joints (39.9% and 50.4% for RSW, 31.7% and 35.0% for CCL). With one exception, the load-bearing capacity of the CCL joints is higher than that of the RSW joints (156.1–108.3%).