The genus Ganoderma has a long history of use in traditional Asiatic medicine due to its different nutritional and medicinal properties. In Mexico, the species G. tuberculosum is used in indigenous communities, for example, the Wixaritari and mestizos of Villa Guerrero Jalisco for the treatment of diseases that may be related to parasitic infections; however, few chemical studies corroborate its traditional medicinal potential. Thereby, the objective of this study was to isolate and identify anti-parasitic activity compounds from a strain of G. tuberculosum native to Mexico. From the fruiting bodies of G. tuberculosum (GVL-21) a hexane extract was obtained which was subjected to guided fractioning to isolate pure compounds. The in vitro anti-parasitic activity of the pure compound (IC50) was assayed against Leishmania amazonensis, Trypanosoma cruzi, Acanthamoeba castellanii Neff, and Naegleria fowleri. Furthermore, the cytotoxicity (CC50) of the isolated compounds was determined against murine macrophages. The guided fractioning produced 5 compounds: ergosterol (1), ergosta-4,6,8(14),22-tetraen-3-one (2), ergosta-7,22-dien-3β-ol (3), 3,5-dihydroxy-ergosta-7,22-dien-6-one (4), and ganoderic acid DM (5). Compounds 2 and 5 showed the best anti-parasitic activity in an IC50 range of 54.34 ± 8.02 to 12.38 ± 2.72 µM against all the parasites assayed and low cytotoxicity against murine macrophages. The present study showed for the first time the in vitro anti-parasitic activity of compounds 1-5 against L. amazonensis, T. cruzi, A. castellanii Neff, and N. fowleri, corroborating the medicinal potential of Ganoderma and its traditional applications.