In the condensation methods of peptide segments so-called the thioester method, protecting groups for amino and thiol groups are generally required for the regioselective ligation. Recently, we found that azido group could be used as an amino protecting group on the peptide condensation reaction. Azido group could be easily converted into amino group by reduction using Zn/AcOH. On the other hand, acetamidomethyl (Acm) group has been generally used for the thiol protection. However, Acm group is stable under reducing conditions, and an additional deprotection step for cleaving Acm group after the reduction is required to obtain the unprotected polypeptide. In this paper, we demonstrate that phenacyl (Pac) group could be used as an efficient protecting group of cysteine side chains. We synthesized cysteine derivative carrying Pac group at the side chain sulfur atom [Fmoc-Cys(Pac)-OH] at first, and Pac-containing peptides and peptide thioesters were synthesized using it by the ordinary 9-fluorenylmethoxycarbonyl (Fmoc)-based solid-phase peptide synthesis (SPPS) strategy. When using N,N’-dicyclohexylcarbodiimide (DCC)/1-hydroxybenzotriazole (HOBt) as condensation reagents in SPPS, coupling efficiency of the amino acid next to the Cys(Pac) was low. On the other hand, when 2-(1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate (HBTU)/N,N-diisopropylethylamine (DIEA) was used as condensation reagents instead of DCC/HOBt, the Fmoc-amino acid could be introduced efficiently, and the yield of peptide was improved. Pac-containing peptide segments could be condensed by the thioester method. After the condensation reaction, Pac groups could be removed by Zn/AcOH treatment. In addition, the azido group at the lysine side chain was simultaneously converted to an amino group, demonstrating that this protecting group scheme simplified the deprotecting reaction after the peptide condensation reaction to only one step.