In vascular surgical applications, small-diameter vascular grafts made from synthetic polymers are rarely commercialized, owing to delayed reendothelialization and subsequent thrombus formation and occlusion. Here, we describe a novel design for a small-diameter poly-ε-caprolactone (PCL) vascular graft with a functional, bilayered nanofibrous structure and a composition that enables a suitable healing process and gradual degradation/replacement by natural blood vessels. To improve vascular cell responses to the PCL, a natural bioactive polymer (collagen) and a sol–gel-derived bioceramic (silica) were incorporated into the inner and outer layer of the PCL vascular graft, respectively. An electrospinning technique enabled the development of uniform electrospun PCL/collagen and PCL/silica nanofibers. In particular, the orientations of PCL/collagen nanofibers prepared with a high-speed rotating collector were highly aligned, and no breaks or irregular shapes were observed. The thin inner layer, composed of PCL/collagen with longitudinally aligned nanofibers, was favorable for the adhesion, elongation, and migration of endothelial cells, thus eliciting rapid reendothelialization of luminal surfaces of a vascular graft. The relatively thick outer layer, composed of PCL/silica with randomly distributed nanofibers, provided a superior mechanical strength and showed satisfactory biocompatibility. The findings of this study demonstrate a strong potential of PCL-based bilayer vascular grafts for vascular tissue applications.