Chromatographic separation of an ethyl acetate extract from Embelia schimperi led to the isolation of a new compound identified as 2,5-dihydroxy-3-methyl-1,4-benzoquinone (1) on the basis of spectroscopic and physical data. The plant’s crude extract and pure compound 1 were assayed for in vitro antimicrobial activity against clinical strains of Salmonella spp., Proteus spp., Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Cryptococcus neoformans, Shigella dysentriae and Staphylococcus aureus. Disc diffusion method was used and zones of inhibition, after respective incubation periods, were used to quantify antimicrobial activity. Standard antibiotics namely: augmentin, cotrimoxazole, gentamycin, tetracycline and lyncomycin were used as controls. The crude extract was inactive while the pure compound 1 showed significant activities against Salmonella spp., Proteus spp., Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Cryptococcus neoformans, Shigella dysentriae and Staphylococcus aureus with zones of inhibition ranging from 10−20 mm. The most sensitive microorganism was P. aeruginosa while C. neoformans was insensitive to both the crude extract and compound 1.