Background and Aim: Blastocystis hominis is an intestinal protozoan in humans and animals. The parasite causes mild-to-severe intestinal complications, such as diarrhea, in healthy humans and immunocompromised hosts. This study aimed to determine the antiprotozoal activity of Boesenbergia rotunda (L.) Mansf and Ganoderma lucidum (Fr.) Kart extracts against B. hominis. Materials and Methods: Antiprotozoal activity of B. rotunda and G. lucidum extracts against B. hominis subtype 3 was determined using the erythrosin B exclusion assay, confirmed by a time-kill study. The morphology of the parasite treated with the extracts was observed by a scanning electron microscope. The phytochemicals present in B. rotunda and G. lucidum extracts were identified by gas chromatography-mass spectrometry analysis. Results: Both B. rotunda and G. lucidum extracts demonstrated strong antiprotozoal activity with similar minimum inhibitory concentration (MIC) values of 62.5 μg/mL. At 4× MIC and 8× MIC, both B. rotunda and G. lucidum extracts, and metronidazole inhibited the growth of B. hominis by up to 90% after 12 h treatment. Blastocystis hominis cells treated with B. rotunda extract, G. lucidum extract, and metronidazole were deformed and withered when compared with the control. Geraniol and versalide were found as the main compounds in B. rotunda and G. lucidum extracts, respectively. Conclusion: These results indicate the potential medicinal benefits of B. rotunda and G. lucidum extracts in the growth inhibition of B. hominis.