Most structural components undertake cyclic loads in engineering and failures always cause catastrophic economic losses and casualties. In the present work, the phase evolution of Al-Si coating of high-strength boron steel during hot stamping was investigated. Two types of 1500 MPa grade boron steel sheets, one with Al-Si coating and the other without, were studied to reveal the effect on the high-cycle fatigue behavior. The as-received continuously hot-dip Al-Si coating was composed of α(Al), eutectic Al-Si and τ5. After hot stamping at 1193 K, three phases formed in this coating: β2, Fe(Al,Si)2 and α(Fe). The experimental results showed that the endurance limit of the coated steel sheet was 370 MPa under 107 fully reversed tension-compression loading cycles as opposed to 305 MPa in the uncoated sheet. Both the coated and the uncoated specimens showed surface-induced transgranular fatigue fractures. In the uncoated sheet, the fatigue cracks were generated from the decarburization surface, but the Al-Si coating effectively prevented the occurrence of near-surface decarburization during high-temperature hot stamping, and the only cracks in the coated steel sheet were initiated at wire-cutting surfaces.