Electrocatalytic reduction of oxygen plays a crucial role in many energy storage and conversion devices. Currently, the development of high-performance carbon-based non-precious-metal (NPM) oxygen reduction reaction (ORR) catalysts in acidic media still remains a great challenge. Herein, we report a highly active meso/microporous Fe–N-doped carbon nanofiber (Fe–N-CNF) catalyst prepared via a SiO2-protected shell mediated template method. The SiO2-protected shell not only restricts the free migration of iron species but also traps volatile gaseous substances during the pyrolysis process at high temperature, thus leading to a simultaneous optimization of both the surface functionalities and porous structures of the Fe–N-CNF catalysts. Compared to catalysts prepared without a SiO2-protected shell, the Fe–N-CNF catalysts exhibit a much enhanced ORR activity in an acidic medium, along with a superior long-term stability.