A series of chemotherapeutics comprising 2-(4-(5-cyano-2-(methylthio)-6-oxo-1,6-dihydropyrimidin-4-yl)phenoxy)-N-phenylacetamide derivatives (4a -4i) was synthesized, characterized and evaluated for antiprotozoal activity. These compounds were screened for the anti-amoebic potential for which HM1:IMSS strain of Entamoeba histolytica was taken and metronidazole (MTZ) was used as reference amoebicidal drug. Among the nine dihydropyrimidine-phenylacetamide derivatives, five were recorded with better anti-amoebic activity i.e. lower IC50 (0.12 μM to 0.82 μM) values than MTZ (IC50 = 1.8 μM). All the nine compounds displayed minimal antimalarial activity with more than 43% inhibition, with a low toxicity profile against three cell lines; human cell lines, Artemia and host red blood cell, but these compounds were more toxic than quinine. These compounds did not exhibit any significant inhibition against the viability of Anopheles arabiensis (KGB) larvae or ova. Docking study provided good binding affinity when interacted with the enzyme O-acetyl-L-serine sulfohydrolase (EhOASS) of E. histolytica ( PDB id: 3BM5). These studies demonstrated the dihydropyrimidin-acetamide derivatives to be better anti-amoebic agents.