Separation and determination of dopamine and epinephrine with end-channel electrochemical (EC) detection integrated on a native printed microchip capillary electrophoresis (CE) system was investigated. Factors influencing the separation and detection were investigated and optimized. Results show manipulating EOF, which can be easily achieved by adjusting buffer pH, is a simple and effective way to achieve the baseline separation of dopamine and epinephrine in native polymeric microchips. Without surface modification of microchannel, printed microchips with advantages of low cost and easy preparation can achieve high performance like other microfluidic devices.