The medicinal plant Brucea javanica (L.) Merr. (Simaroubaceae), grown in China, was examined for anti-babesial properties. The anti-babesial activity of the fruit was found to be attributed to its quassinoid constituents. Ten active compounds were isolated and purified from a chloroform extract. The identities of these compounds were confirmed from NMR spectroscopic and mass spectral data as brusatol (1), bruceantin (2), bruceine A (3), bruceantinol (4), dehydrobruceine B (5), dehydrobrusatol (6), dehydrobruceine A (7), bruceine D (8), bruceoside A (9), and yadanzioside G (10). When tested in vitro against Babesia gibsoni, compounds 1–10 had IC50 values of 0.74, 13.4, 4.0, 12.0, 308.2, 10.5, 835.0, >1000, and >1000 ng/mL, respectively. Compounds 1–4, 6 and 7 had far higher activity than the commercial anti-babesial drug diminazene aceturate, which possesses an IC50 value of 70.5 ng/mL. Except for bruceine A (3), bruceantinol (4) and bruceine D (8), this is the first report of the anti-babesial activity of these isolated quassinoids.