Methicillin-resistant Staphylococcus aureus (MRSA) is a dangerous microorganism, and creates serious medical problems. It causes many types of infections in humans and often acquires multi-drug resistance. In this study, silibinin was evaluated against 20 clinical isolates of MRSA, either alone or in combination with ampicillin or oxacillin, using a checkerboard assay. The silibinin exhibited good activity against isolates of MRSA, and MRSA ATCC33952 and MSSA ATCC25923, with minimum inhibitory concentrations/minimum bactericidal concentrations (MICs/MBCs) ranging between 2–8/4–16 μg/mL, for ampicillin 2–1024/2–2048 μg/mL, and for oxacillin 0.25–32/0.5–64 μg/mL. The range of MIC50 and MIC90 were 0.5–4 μg/mL and 2–8 μg/mL, respectively. The MICs/MBCs for the combination of silibinin plus oxacillin or ampicillin were reduced by ≥4-fold against the MRSA isolates tested, demonstrating a synergistic effect, as defined by a fractional inhibitory concentration index (FICI) of ≤0.5. Furthermore, a time-kill study evaluating the growth of the tested bacteria showed that growth was completely attenuated after 2–5 h of treatment with the 1/2 MIC of silibinin, regardless of whether it was administered alone or with oxacillin (1/2 MIC) or ampicillin (1/2 MIC). In conclusion, silibinin exerted synergistic effects when administered with oxacillin or ampicillin and the antibacterial activity and resistant regulation of silibinin against clinical isolates of MRSA might be useful in controlling MRSA infections.