Background: At present, the emergence and spread of antimalarial drug resistance has become a significant problem worldwide. There has been a challenge in searching for natural products for the development of novel antimalarial drugs. Therefore, this study aims to evaluate compounds fromDioscorea bulbiferaresponsible for antimalarial properties and investigate potential interactions of the compounds withPlasmodium falciparumlactate dehydrogenase (PfLDH), an essential glycolytic enzyme in the parasite’s life cycle.Methods: An in vitro study of antimalarial activity against chloroquine (CQ)-resistantPlasmodium falciparum(K1 strain) and CQ-sensitiveP. falciparum(3D7 strain) was performed using the3H-hypoxanthine uptake inhibition method. The cytotoxic effects of the pure compounds were tested against Vero cells using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The interactions of the compounds with thePfLDH active site were additionally investigated using a molecular docking method.Results: Quercetin (6) exhibited the highest antimalarial activity against theP. falciparumK1 and 3D7 strains, with IC50values of 28.47 and 50.99 μM, respectively. 2,4,3′,5′-Tetrahydroxybibenzyl (9), 3,5-dimethoxyquercetin (4) and quercetin-3-O-β-D-galactopyranoside (14) also possessed antimalarial effects against these two strains ofP. falciparum. Most pure compounds were nontoxic against Vero cells at a concentration of 80 μg/ml, except for compound 9, which had a cytotoxic effect with a CC50value of 16.71 μM. The molecular docking results indicated that 9 exhibited the best binding affinity to thePfLDH enzyme in terms of low binding energy (− 8.91 kcal/mol) and formed strong hydrogen bond interactions with GLY29, GLY32, THR97, GLY99, PHE100, THR101 and ASN140, amino acids as active sites. In addition, 6 also possessed remarkable binding affinity (− 8.53 kcal/mol) toPfLDH by interacting with GLY29, ILE31, ASP53, ILE54, THR97 and THR101.Conclusion: Quercetin is a major active compound responsible for the antimalarial activity ofD. bulbiferaand is an inhibitor ofPfLDH. These findings provide more evidence to support the traditional use ofD. bulbiferafor malaria treatment. Structural models of its interactions at thePfLDH active site are plausibly useful for the future design of antimalarial agents.