The demand for electrically insulated microwires and microfibers in biomedical applications is rapidly increasing. Polymer protective coatings with high electrical resistivity, good chemical resistance, and a long shelf-life are critical to ensure continuous device operation during chronic applications. As soft and flexible electrodes can minimize mechanical mismatch between tissues and electronics, designs based on flexible conductive microfibers, such as carbon nanotube (CNT) fibers, and soft polymer insulation have been proposed. In this study, a continuous dip-coating approach was adopted to insulate meters-long CNT fibers with hydrogenated nitrile butadiene rubber (HNBR), a soft and rubbery insulating polymer. Using this method, 4.8 m long CNT fibers with diameters of 25–66 µm were continuously coated with HNBR without defects or interruptions. The coated CNT fibers were found to be uniform, pinhole free, and biocompatible. Furthermore, the HNBR coating had better high-temperature tolerance than conventional insulating materials. Microelectrodes prepared using the HNBR-coated CNT fibers exhibited stable electrochemical properties, with a specific impedance of 27.0 ± 9.4 MΩ µm2at 1.0 kHz and a cathodal charge storage capacity of 487.6 ± 49.8 mC cm−2. Thus, the developed electrodes express characteristics that made them suitable for use in implantable medical devices for chronic in vivo applications.