A novel aptamer-based CE with chemiluminescence (CL) assay was developed for highly sensitive detection of human immunoglobulin E (IgE). The IgE aptamer was conjugated with gold nanoparticles (AuNPs) to form AuNPs-aptamer that could specifically recognize the IgE to produce an AuNPs-aptamer-IgE complex. The mixture of the AuNPs-aptamer-IgE complex and the unbounded AuNPs-aptamer could be effectively separated by CE and sensitively detected with luminol-H2O2 CL system. By taking the advantage of the excellent catalytic behavior of AuNPs on luminol-H2O2 CL system, the ultrasensitive detection of IgE was achieved. The detection limit of IgE is 7.6 fM (S/N = 3) with a linear range from 0.025 to 250 pM. Successful detection of IgE in human serum samples was demonstrated and the recoveries of 94.9-103.2% were obtained. The excellent assay features of the developed approach are its specificity, sensitivity, adaptability, and very small sample consumption. Our design provides a methodology model for determination of rare proteins in biological samples.