A new synthetic method for peptide thioesters is described using Fmoc solid-phase peptide synthesis (Fmoc-SPPS). This method employs a novel enamide motif to facilitate irreversible intramolecular N-to-S acyl migration, which can efficiently afford the desired peptide thioesters (3 h, 30 °C) under the final trifluoroacetic acid (TFA) cleavage conditions. The acyl-transfer-mediated approach for synthesis of peptide thioesters tolerated different C-terminal residues and was used to synthesize human C-C motif chemokine 11 (hCCL11) via native chemical ligation.