Increased efflux due to over-expression of efflux pump is a common mechanism of multidrug resistance in Staphylococcus aureus. More recognized resistance mechanisms have eclipsed the contribution of efflux pumps to resistance in S. aureus. This research aimed to assess the efficacy of combining berberine and palmatine with ciprofloxacin in treating S. aureus infections obtained from wounds. The microtiter plate tests were used to study the antimicrobial susceptibility pattern, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) of ciprofloxacin, berberine, and palmatine. The EP inhibition and accumulation assays were performed with a combination of plant extract and ciprofloxacin. Eighty (80) S. aureus isolates were collected from the burn infections. Out of 80 isolates, 76.25 % were resistant to cloxacillin and erythromycin. Also, 1.25 % of S. aureus isolates were resistant to clindamycin and teicoplanin. Likewise, 65%, 21.25%, and 1.25% were considered MDR, XDR, and PDR strains, and 90% of S. aureus isolates were MRSA. The norA, norB, norC, and mecA were reported in 67.5%, 91.25 %, and 90 % of isolates, respectively. Based on the ciprofloxacin-resistant strains (72.5%), the MIC range of berberine and palmatine extracts in 27 isolates (33.7%) was 16 µg/mL to 64 µg/mL. After the combination, the MIC of ciprofloxacin was reduced more than 10-fold in resistant strains. A significant relationship was reported between the combination of plant extract and ciprofloxacin in resistant isolates (p<0.05). The best results of combining berberine, palmatine extract, and ciprofloxacin were observed in MDR, XDR, and PDR strains (p<0.001). Antimicrobial results of berberine and palmatine extracts against S. aureus were observed; however, clinical trials are necessary to confirm the efficiency of these extracts. We reported that combining berberine and palmatine with ciprofloxacin might reduce treatment failure due to EP overexpression.