Fibrous polyurethane-based scaffolds have proven to be promising materials for the tissue engineering of implanted medical devices. Sterilization of such materials and medical devices is an absolutely essential step toward their medical application. In the presented work, we studied the effects of two sterilization methods (ethylene oxide treatment and electron beam irradiation) on the fibrous scaffolds produced from a polyurethane-gelatin blend. Scaffold structure and properties were studied by scanning electron microscopy (SEM), atomic force microscopy (AFM), infrared spectroscopy (FTIR), a stress-loading test, and a cell viability test with human fibroblasts. Treatment of fibrous polyurethane-based materials with ethylene oxide caused significant changes in their structure (formation of glued-like structures, increase in fiber diameter, and decrease in pore size) and mechanical properties (20% growth of the tensile strength, 30% decline of the maximal elongation). All sterilization procedures did not induce any cytotoxic effects or impede the biocompatibility of scaffolds. The obtained data determined electron beam irradiation to be a recommended sterilization method for electrospun medical devices made from polyurethane-gelatin blends.