Sonogashira coupling between diversely substituted 2-benzyloxy-5-bromopyrimidines and various aryl and aliphatic alkynes in the presence of catalytic amount of PdCl2(PPh3)2 with diethylamine and CuI as a co catalyst in THF at 60 °C afforded 17 new 2-benzyloxy-5-alkyne substituted pyrimidines in good yields (85–94 %). The cytotoxic activity of resulted compounds were evaluated against A549 (Human lung adenocarcinoma cell line), HepG2 (Human liver cancer cell line) and HCT116 (Human colon cancer cell line) cancer cell lines. Some of the 2-benzyloxy-5-alkyne pyrimidines synthesized were found to be shown moderate in vitro cytotoxic activity against A549 cell line. © 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim