In this paper we report a kind of fast-scale instability occurring in the single-ended primary inductance converter (SEPIC) power factor pre-regulator, which is designed to operate in discontinuous conduction mode. Main results are given by exact cycle-by-cycle computer simulations as well as theoretical analysis. It is found that the instability phenomenon manifests itself as a fast-scale bifurcation at the switching period, which implies the occurrence of border collision bifurcation, or is related to the transition of the regular operating mode of the SEPIC. According to the theoretical analysis and simulation results, the effects of parameters on system stability, and the locations of the bifurcation points are confirmed. Moreover, the effects of such an instability on power factor and switching stress are also discussed. Finally, the occurrence of the asymmetric bifurcation locations is investigated. The results show that this work provides a convenient means of predicting stability boundaries which can facilitate the selection of the practical parameters.