Nanostructured carbon-based materials fabricated via simple methods from renewable bio-resources have great potential in rechargeable energy storage systems. In this study, nanoporous pyroproteins containing a large amount of redox-active heteroatoms (H-NPs) were fabricated from silk fibroin by an in situ carbonization/activation method. The H-NPs have a large surface area of ∼3050 m2 g−1, which is mainly comprised of nanometer-scale pores. Also, these H-NPs have oxygen and nitrogen heteroatoms of 17.4 wt% and 2.9 wt%, respectively. Synergistic sodium ion storage behaviors originate from electrochemical double layer capacitance and pseudocapacitance, leading to very high electrochemical performances of H-NPs in aqueous and non-aqueous electrolyte systems. Sodium-ion supercapacitors (NISs) based on commercial graphite//H-NPs show a high specific power of ∼1900 W kg−1 at ∼77 Wh kg−1. Also, NISs based on commercial hard carbon//H-NPs exhibit a high specific energy of ∼217 Wh kg−1 at ∼42 W kg−1. In addition, outstanding cycling performances over 30,000 cycles are achieved for symmetric NISs.