We describe a simple and efficient strategy for the selective modification of peptide N-terminus with an unnatural amino acid starting from an unprotected peptide. Selective chemical modification of N-termini of unprotected peptides is challenging due to the presence of various reactive functional groups. We chose to modify N-terminus with a cysteine surrogate that enables NCL of target proteins that lack cysteine at the appropriate position. To begin with, we designed a peptide having SUMO-HisTag-TEV sequence preceding the N-terminus of the target peptide. Recombinant expression in E.coli and subsequent SUMO protease cleavage yielded HisTag-TEV-target peptide. Partial protection of lysine side chains of this peptide with carbohydrate protecting group and removal of HisTag-TEV sequence by TEV protease yielded partially protected peptide with free N-terminal amine. For partial protection, we replaced the conventional tBoc protecting group with carbohydrate protecting group that imparted hydrophilicity to the partially protected peptide. Thus, coupling of selenocysteine selectively at the N-terminus and subsequent acid deprotection of carbohydrate protecting groups yielded a modified peptide that can be used for NCL. As a proof of concept, we further demonstrated modification of longer recombinant peptide HisTag-SUMO-EPO(127-166) which is devoid of TEV sequence. This example shows the efficiency of carbohydrate protecting group over partial protection of longer peptides and provides an alternate route to our strategy. We successfully modified N-terminus of EPO(127-166) with a glycosylated dipeptide, selenocysteinylserine(GalNAc) at the N-terminus. Thus, our strategy demonstrated its potential for the modification of recombinant peptides with any desired unnatural amino acid including glycosylated amino acid. Thus, our strategy expands the semisynthetic toolbox for synthesis of post-translationally modified proteins by NCL method.