A simple and rapid capillary electrophoretic procedure for analysis of matrine and oxymatrine in Kushen medicinal preparations has been developed and optimized. Orthogonal design was used to optimize the separation and detection conditions for the two active components. Phosphate concentration, applied potential, organic modifier content, and buffer pH were selected as variable conditions. The optimized background electrolyte contained 70 mM sodium dihydrogen phosphate and 30% acetonitrile at pH 5.5; the separation potential was 20 kV. Each analysis was complete within 5 min. Regression equations revealed linear relationships (r > 0.999) between peak area and amount for each component. The detection limits were 1.29 μg mL−1 for matrine and 1.48 μg mL−1 for oxymatrine. The levels of the two active compounds in two kinds of traditional Chinese medicinal preparation were easily determined with recoveries of 96.57–106.26%. In addition, multiple linear regression and a non-linear model using a radial basis function neural network approach were constructed for prediction of the migration time of oxymatrine. The predicted results were in good agreement with the experimental values, indicating that a radial basis function neural network is a potential means of prediction of separation time in capillary electrophoresis.