The aim of this study was to develop and validate a simultaneous analytical method for berberine and palmatine, which are representative substances of Phellodendron amurense, and to evaluate the antioxidant activity. We evaluated the specificity, linearity, precision, accuracy, limit of detection (LOD), and limit of quantification (LOQ) of analytical methods for berberine and palmatine using high-performance liquid chromatography. Our result showed that the correlation coefficients of the calibration curve for berberine and palmatine exhibited 0.9999. The LODs for berberine and palmatine were 0.32 to 0.35 μg/mL and the LOQs were 0.97 to 1.06 μg/mL, respectively. The inter-day and intra-day precision values for berberine and palmatine were from 0.12 to 1.93 and 0.19 to 2.89%, respectively. The inter-day and intra-day accuracies were 98.43-101.45% and 92.39-100.60%, respectively. In addition, the simultaneous analytical method was validated for the detection of berberine and palmatine. Moreover, we conducted FRAP and NaNO2 scavenging activity assays to measure the antioxidant activities of berberine and palmatine, and both showed antioxidant activity. These results suggest that P.amurense could be a potential natural resource for antioxidant activity and that the efficacy can be confirmed by investigating the content of the berberine and palmatine.