We described a route to a core-shell polynaphthoxazine nanofiber that can be fabricated by a single-nozzle electrospinning process using a phase-separated mixed polymer composite solution. The naphthoxazine-based polymer, as the core material, was synthesized by using a hydroxyl-containing naphthoxazine through esterification with methacryloyl chloride and subsequent free radical polymerization. Our results demonstrated that these core-shell structure nanofibres are composed of bundles of regularly structured ultrafine polynaphthoxazine nanofibers as the core and polymethylmethacrylate (PMMA) as the shell, because of the incompatibility of the naphthoxazine-based polymer and PMMA in mixed solvents. To maintain the structural integrity of the fibrous network during the curing process, we carried out the curing reaction in a chemically inert fluid with p-toluenesulfonic acid as the catalyst. After carbonization, the obtained carbon fiber with high nitrogen content (2.2 wt%), resulting from the oxazine ring as the carbon source, showed individual nanofibres without aggregation, and with a mean diameter of less than 30 nm. As an energy storage electrode, these naphthoxazine-based carbon nano-materials have excellent high-rate discharge capacity and low equivalent series resistance.