The C1–C17 segment of bafilomycin N has been synthesized. The C1–C11 segment was synthesized by the anti-selective vinylogous Mukaiyama aldol reaction with a chiral vinylketene silyl N,O-acetal and the Horner–Wadsworth–Emmons reaction, whereas C12–C17 was constructed by the syn-selective vinylogous Mukaiyama aldol reaction and the Jung’s semipinacol rearrangement. Those segments were connected by the Stille coupling to afford the C1–C17 segment.