In this study, we synthesized three types of carbon nanofibers doped with transition metals (TM = Fe or Co) and nitrogen (N) using electrospinning and heat treatment procedures, and their activity was measured for the oxygen reduction reaction (ORR) in both acid and alkaline media. It was found that the nanofiber catalysts co-doped with TM and N exhibited higher ORR activity than the metal-free nanofibers doped only with N in both electrolytes. In addition, all three catalysts showed a higher ORR activity in alkaline vs. acid electrolytes. Based on the advanced electron microscopy images in atomic scale and density functional theory calculations, we proposed that the active sites in these catalysts for ORR were the TM-N-4 clusters embedded between two graphene edges and the pyridinic nitrogen derived carbon atoms. Our proposal of ORR active sites explains our electrochemical measurement results. Through this comparative study, we gained new insights into the role of transition metals and electrolytes in affecting the ORR activity of transition metal and nitrogen derived non-precious carbon catalysts.