One-layer wound dressings cannot meet all the clinical needs due to their individual characteristics and shortcomings. Therefore, bilayer wound dressings which are composed of two layers with different properties have gained lots of attention. In the present study, polycaprolactone/gelatin (PCL/Gel) scaffold was electrospun on a dense membrane composed of polyurethane and ethanolic extract of propolis (PU/EEP). The PU/EEP membrane was used as the top layer to protect the wound area from external contamination and dehydration, while the PCL/Gel scaffold was used as the sublayer to facilitate cells’ adhesion and proliferation. The bilayer wound dressing was investigated regarding its microstructure, mechanical properties, surface wettability, anti-bacterial activity, biodegradability, biocompatibility, and its efficacy in the animal wound model and histopathological analyzes. Scanning electron micrographs exhibited uniform morphology and bead-free structure of the PCL/Gel scaffold with average fibers’ diameter of 237.3 ± 65.1 nm. Significant anti-bacterial activity was observed against Staphylococcal aureus (5.4 ± 0.3 mm), Escherichia coli (1.9 ± 0.4 mm) and Staphylococcus epidermidis (1.0 ± 0.2 mm) according to inhibition zone test. The bilayer wound dressing exhibited high hydrophilicity (51.1 ± 4.9°), biodegradability, and biocompatibility. The bilayer wound dressing could significantly accelerate the wound closure and collagen deposition in the Wistar rats’ skin wound model. Taking together, the PU/EEP-PCL/Gel bilayer wound dressing can be a potential candidate for biomedical applications due to remarkable mechanical properties, biocompatibility, antibacterial features, and wound healing activities.