A new series of 5‐fluoro‐N4‐(3‐(4‐substitutedbenzylamino)phenyl)‐N2‐(4‐morpholinophenyl)pyrimidine‐2,4‐diamine derivatives (7a, 7b, 7c, 7d, 7e, 7f, 7g, 7h, 7i, 7j) are prepared from using an intermediate compound 5‐fluoro‐N4‐(3‐(aminophenyl)‐N2‐(4‐morpholinophenyl)pyrimidine‐2,4‐diamine (5). The structures of the newly synthesized products are established from their spectral 1H‐NMR, 13C‐NMR, 19F‐NMR, ESI‐MS, and analytical data. Here we report the synthesized compounds and larvicidal activity. All the compounds are screened for their significant larvicidal activity against third instar larvae at 24, 48, and 78‐h time exposure, and values were compared with standard drug Malathion. The Compounds 7i, 7a, 7c, 7f, and 7j exhibited significant activity. However the compounds 7b, 7e, 7d, and 7h showed excellent activity when compared to the above compounds and to standard drug malathion too because of the presence of mild electron withdrawing groups such as trifluoro, fluorine, hydroxy, nitro, and methoxy derivatives which are attached to the benzyl ring.