Biofluidic open-type supercapacitors offer significant advantages over batteries in implantable electronics. However, poor energy storage in bioelectrolytes and performance degradation owing to electrode biofouling remain challenges and hamper their implementation. In this study, we present a flexible polydopamine (PDA)-infiltrated carbon nanotube (CNT) yarn (PDA/CNT) supercapacitor with high performance in biofluids, encapsulated by a hydrogel-barrier circular knit that provides anti-biofouling protection. Infiltration of the biopolymer PDA provide a hydrophilic coating to obtain a hydrophobic CNT electrode under aqueous conditions and an energy density 250-fold higher than that of the pristine CNT in the biofluid. The PDA/CNT supercapacitor exhibited remarkable energy performance in biological fluids in terms of the maximum areal capacitance (503.91 mF cm-2), energy density (274 μWh/cm2), and power density (25.52 mW cm-2). Moreover, it demonstrated negligible capacitance loss after 10,000 repeated charge/discharge cycles and bending tests. To prevent biofouling, the PDA/CNT electrode was encapsulated in an agarose-coated circular knit that allows free movement of the electrolyte. Notably, implanting an encapsulated PDA/CNT supercapacitor into the abdominal cavity of rat resulted in stable in vivo energy storage performance without biofouling for 21 d, and the charged supercapacitor was used successfully to power a light-emitting diode in vivo.