Herein, we present the synthesis of porous polyaniline (PANI) nanofiber networks by a chemical oxidative polymerization method using a biomolecule, heparin. Long uniform nanofibers were formed when the weight ratio of heparin to aniline was 0.25 (PANIH-0.25), where the average nanofiber diameter was about 80–110 nm. No such PANI nanofibers were formed at other weight ratios. A comparison of the morphology of PANIH-0.25 was made with the pure PANI which was synthesized without any template. We further studied the potential of PANIH-0.25 as a nanostructured electrode material for the supercapacitor applications. The PANIH-0.25 nanofiber electrode yielded a six-fold improvement in specific capacitance when compared with pure PANI. The PANIH-0.25 electrode exhibited a specific capacitance of 732.18 ± 24.1 F g⁻¹ and a longer cycle life with the capacitance retention of 72.28% after 1000 cycles. The observed capacitance was elucidated and justified based on theoretical considerations.