In the synthesis of cetrorelix via solid-phase peptide synthesis (SPPS) employing the Fmoc strategy, the racemization of L-arginine and L-serine was effectively minimized to below 0.5%. This reduction was achieved using the coupling agent HATU, the additive HOBt or HOAt, and the base TMP. Racemization was observed during the coupling of Fmoc-L-arginine(Pbf) and Fmoc-O-tert-butyl-L-serine on Rink Amide AM resin. A gradient reversed-phase high-performance liquid chromatography (RP-HPLC) method was developed for the separation of all the structurally closely related cetrorelix isomers. Optimized RP-HPLC conditions identified D-arginine and D-serine isomeric impurities as the closest eluting peaks to the main cetrorelix peak. Controlling these impurities to the lowest possible levels is essential for developing an efficient preparative HPLC purification process for the commercial production of cetrorelix. This stringent control ensures that the final product meets the high standards required for commercial production and therapeutic use.