The methanolic extract of the rhizomes parts of Agelica purpuraefolia was investigated for its activity against chloroquine‐sensitive strains of Plasmodium falciparum using the parasite lactate dehydrogenase assay method. Two natural khellactone, (+)‐4′‐Decanoyl‐cis‐khellactone (1) and (+)‐3′‐Decanoyl‐cis‐khellactone (2) were isolated from the rhizomes parts of A. purpuraefolia. Two compounds were evaluated for in vitro antiplasmodial activities as well as their cytotoxic potential on SK‐OV‐3 cancer cell line cells. Compounds 1, 2 showed notable growth inhibitory activity against chloroquine‐sensitive strains of Plasmodium falciparum with IC50 values from 1.5 and 2.4 μM. This compound showed no significant cytotoxicity (IC50 > 100 μM) evaluated using SK‐OV‐3 cancer cell line cells. This is the first report on the antiplasmodial activity of the compounds from A. purpuraefolia. Copyright © 2009 John Wiley & Sons, Ltd.