Background: The gastrointestinal parasite Giardia lamblia causes giardiasis. Its treatment with standard drugs produces side effects and improper treatment can generate resistant strains. New antigiardial compounds are needed. An analysis was done to identify the antigiardial activity of Morinda royoc, a plant used in traditional Mayan medicine to treat stomach and bowel pain. We aimed to assess the efficacy of M. royoc roots against G. lamblia and their effect on cells viability. Methods: A methanol extract was done of the root and then fractionated. The extract and fractions were tested in vitro on G. lamblia trophozoites and their effect on cell viability was quantified by flow cytometry. The active extract and fractions were analyzed by gas chromatography–mass spectrometry and high-performance liquid chromatography. Results: The hexane fraction exhibited potent activity against G. lamblia (IC50 = 0.08 µg/mL). Its principal component was an anthraquinone-type compound. None of the fractions were toxic to human promyelocytic leukemia, chronic myelogenous leukemia and human mononuclear cells. Conclusion: The medicinal plant M. royoc contains promising bioactive agents with antigiardial activity and deserves further research.