A series of novel 4-aminoquinoline-pyrimidine hybrids has been synthesized and evaluated for their antimalarial activity. Several compounds showed promising in vitro antimalarial activity against both CQ-sensitive and CQ-resistant strains with high selectivity index. All the compounds were found to be non-toxic to the mammalian cell lines. Selected compound 7g exhibited significant suppression of parasitemia in the in vivo assay. The heme binding studies were conducted to determine the mode of action of these hybrid molecules. These compounds form a stable 1:1 complex with hematin suggesting that heme may be one of the possible targets of these hybrids. The interaction of these conjugate hybrids was also investigated by the molecular docking studies in the binding site of PfDHFR. The pharmacokinetic property analysis of best active compounds was also studied using ADMET prediction. Novel 4-aminoquinoline-pyrimidine hybrids were synthesized and evaluated for antimalarial activity against D6 and W2 strains of Plasmodium falciparum. Certain compounds showed better activity than the parent compounds against both strains. Display omitted •A series of novel hybrid molecules of 4-aminoquinoline-pyrimidine were synthesized.•Antimalarial activity against both CQS-D6 and CQR-W2 strains of Plasmodium falciparum was demonstrated at micromolar level.•One compound showed moderate activity in vivo.•Compounds showed effective binding with heme in 1:1 complex.•Molecular docking studies and ADMET properties were investigated.