In this report, a novel carbon nanotube/poly(ethylene-co-vinyl acetate) (CNT/EVA) composite electrode was developed for the amperometric detection in CE. The composite electrode was fabricated by packaging a mixture of CNTs and melted EVA in a piece of fused-silica capillary under heat. it was coupled with CE for the separation and detection of esculin and esculetin in Cortex Fraxini, a traditional Chinese medicine, to demonstrate its feasibility and performance. Esculin and esculetin have been well separated within 9 min in a 40 cm long capillary at a separation voltage of 12 kV using a 50 mM borate buffer (pH 9.2). The new CNT-based CE detector offered significantly lower detection potentials, yielded enhanced SIN characteristics, and exhibited high resistance to surface fouling and enhanced stability. It showed long-term stability and reproducibility with relative standard deviations of less than 5% for the peak current (n = 15) and should also find a wide range of applications in other microfluidic analysis systems.