We report a novel on-line electrophoretic sample clean-up approach for highly sensitive and reproducible microchip electrophoretic (μCE) immunoassay of low-abundance proteins in human serum. The method takes advantage of the differential effect of field-amplified sample stacking on molecules with different electrophoretic mobility. Large interfering proteins are removed from the loading channel by simple voltage control, resulting in selective concentration and injection of smaller target analytes to the separation channel. As a proof of concept, an antibody-free injection mode was developed for direct μCE immunoassay of human insulin-like growth factor-I (IGF-I) in serum samples without any additional purification steps. Clear and sharp peaks were obtained for IGF-I with low background and excellent reproducibility. Besides, the assay sensitivity was further increased by addition of ethanol to the sample buffer at a concentration of 50% right before performing the μCE detection. The lower limit of detection of IGF-I achieved 0.68 ng mL−1, with an overall signal enhancement factor of 2750. The established on-line electrophoretic sample clean-up approach may find wide applications in the development of other microchip-based high-throughput analytical platforms for clinical and biological use.