Fructus Euodiae is used in Traditional Chinese Medicine to treat infection. In this study, four of the quinolone alkaloids isolated from Fructus Euodiae showed activity against methicillin-resistant Staphylococcus aureus (MRSA). The minimum inhibitory concentrations (MIC) were 8–128 µg/mL, which were equivalent to or lower than the control antibiotics, oxacillin, erythromycin and tetracycline (MIC ≥128 µg/mL). Among these isolated quinolone alkaloids, evocarpine with a 13 carbon alkenyl chain substituent at position-2 showed the best activity against MRSA. This study has demonstrated the potential of quinolone alkaloids from Fructus Euodiae as anti-MRSA compounds and supports the traditional use of the fruit as a treatment for bacterial infections.