To use implantable biomedical devices such as electrocardiograms and neurostimulators in the human body, it is necessary to package them with biocompatible materials that protect the internal electronic circuits from the body’s internal electrolytes and moisture without causing foreign body reactions. Herein, we describe a hydrogel surface-modified polyurethane copolymer film with concurrent water permeation resistance and biocompatibility properties for application to an implantable biomedical device. To achieve this, hydrophobic polyurethane copolymers comprising hydrogenated poly(ethylene-co-butylene) (HPEB) and aliphatic poly(carbonate) (PC) were synthesized and their hydrophobicity degree and mechanical properties were adjusted by controlling the copolymer composition ratio. When 10 wt% PC was introduced, the polyurethane copolymer exhibited hydrophobicity and water permeation resistance similar to those of HPEB; however, with improved mechanical properties. Subsequently, a hydrophilic poly(vinyl pyrrolidone) (PVP) hydrogel layer was formed on the surface of the polyurethane copolymer film by Fenton reaction using an initiator and crosslinking agent and the effect of the initiator and crosslinking agent immobilization time, PVP concentration and crosslinking agent concentration on the hydrogel properties were investigated. Finally, MTT assay showed that the hydrogel surface-modified polyurethane copolymer film displays excellent biocompatibility.