The increasing demand for biocompatible bone substitutes has made it a priority to tissue engineering and regenerative medicine scientists. Combination of minerals, growth factors, and extracellular matrix (ECM) proteins with nanofibrous scaffolds is a potential promising strategy for bone reconstruction and clinical applications. In this study, nanohydroxyapatite (nHA) was incorporated in electrospun nanofibrous polycaprolactone (PCL) scaffolds coated with fibronectin (Fn). The potential bone regeneration capacities of these scaffolds were evaluated in vitro and in vivo using mouse mesenchymal stem cells (mMSCs). The interconnected pores and proper mechanical characteristics of the fabricated electrospun PCL mats in combination with nHA and Fn provided suitable environment for cell attachment, proliferation, and enhanced osteogenic differentiation. The synergistic effect of Fn and nHA on the both in vitro and in vivo increase of calcium deposition was assessed by biochemical analysis. In addition, alkaline phosphatase (ALP) activity in nHA-incorporated PCL scaffold (PCL/nHA) and Fn-coated PCL/nHA (PCL/nHA/Fn) were significantly higher in comparison to the control group. Quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) analyses of important bone-related genes (ALP, osteocalcin, osteopontin, and Runx2) revealed that Fn has additive effect on promoting the osteogenic differentiation. The aforementioned results indicated that nanofibrous PCL/nHA scaffold coated with Fn is a promising candidate for bone-tissue engineering applications.