A novel and sensitive method for the determination of amoxicillin (AM) in human urine has been established using capillary electrophoresis (CE) coupled with electrochemiluminescence (ECL) detection, based on the ECL enhancement of Tris(2,2′-bipyridyl) ruthenium(II) with AM. The effects of several factors such as the detection potential, the concentration and the pH of phosphate buffer, the electrokinetic voltage and the injection time were investigated. Under the optimal conditions, the linear concentration of AM ranged from 1.0 ng/ml to 8.0 μg/ml (with a correlation coefficient of 0.9999). The limit of detection was 0.31 ng/ml. The mean recovery was 95.77% with relative standard deviations of no larger than 2.2%. This method is quick (the total run time within 6 min). This method has been successfully applied to a pharmacokinetic study in human urine after oral administration of AM.