The quinolinyl chalcones series (A1–A14) were screened for antimalarial activity. According to in vitro antimalarial studies, many quinolinyl chalcones are potentially active against CQ-sensitive and resistance P. falciparum strains with no toxicity against Vero cell lines. The most active quinolinyl chalcones A4 (with IC50 0.031 μM) made a stable A4–heme complex with − 25 kcal/mole binding energy and also showed strong π–π interaction at 3.5 Å. Thus, the stable A4–heme complex formation suggested that these quinolinyl chalcones act as a blocker for heme polymerization. The docking results of quinolinyl chalcones with Pf-DHFR showed that the halogenated benzene part of quinolinyl chalcones made strong interaction with Pf-DHFR as compared to quinoline part. A strong A4–Pf-DHFR complex was formed with low binding energy (− 11.04 kcal/mole). The ADMET properties of quinolinyl chalcones were also studied. The in vivo antimalarial studies also confirmed the A4 as an active antimalarial agent.