Background: Blastocystis hominis are anaerobic protozoan parasites that belong to the family stramenopiles. They are found in the human large intestine and infect a variety of vertebrates. Objectives: The aim of this study was to evaluate the effect of methanol extract of sea cucumber on induction of apoptosis in Blastocystis hominis cysts in order to introduce a novel potential drug combination. Methods: After mass proliferation of Blastocystis hominis cysts in RPMI1640 medium, 100 µL of sea cucumber extracts with the concentrations ranged from 1 µg/mL to 256 µg/mL and 100 µL of parasite culture medium containing 1.5 × 10 5 cells were added to 96 well plates. The plates were kept at 37°C for 24, 48 and 72 hours exposure and then the effect of the extracts was assessed using MTT assay. To differentiate between apoptosis and necrosis, the inhibitory concentration (IC50) of the extract was determined after 72 hours using flow cytometry and DNA fragmentation tests. Results: The value of IC50 after the exposure of the parasites with different concentrations of the methanol extracts for 24, 48 and 72 hours were 219, 56 and 21 µg/mL, respectively. The occurrence of apoptosis was shown after 72 hours exposure of the parasites to the extract with a concentration of 21 µg/mL using flow cytometry and DNA fragmentation tests. Conclusions: This study showed that methanol extract of sea cucumber can induce apoptosis in Blastocystis hominis. Therefore, further studies for determining the effectiveness of this extract in vivo condition can help to achieve an appropriate drug combination for treatment of Blastocystis hominis.