We have studied the "S-acyl isopeptide method" for the synthesis of peptides containing difficult sequences. The S-acyl isopeptide, which contains a beta-thioester instead of the native N-acyl bond at a Cys residue, can be converted into the target peptide via an S-to-N intramolecular acyl migration reaction. However, the synthesis of the S-acyl isopeptide structure by Fmoc-based SPPS is hampered by repetitive base treatments; decomposition of the thioester and the epimerization of the thioesterified residue are commonly observed. Here, we adopted allyloxycarbonyl (Aloc) protective group to avoid the problem. Catalytic amount of Pd in the presence of scavengers such as PhSiH3 and dimedone selectively removed the Aloc group with neither decomposition of the thioester structure nor epimerization at the thioesterified residue. A model pentapeptide and amylin(1-12) with difficult sequences were efficiently synthesized by the improved S-acyl isopeptides method. Finally, the isolated S-acyl isopeptides were quantitatively converted into the desired peptides via the S-to-N intramolecular acyl migration reaction. The S-acyl isopeptide method will be a usefuI method to prepare the difficult sequence-containing peptides with Cys residue.