Controlled pore size and desirable internal architecture of bone scaffolds play a significant role in bone regeneration efficiency. In addition to choosing appropriate materials, the manufacturing method is another significant factor in fabricating the ideal scaffold. In this study, scaffolds were designed and fabricated by the fused filament fabrication (FFF) technique. Polycaprolactone (PCL) and composites films with various percentages of hydroxyapatite (HA) (up to 20%wt) were used to fabricate filaments. The influence of (HA) addition on the mechanical properties of filaments and scaffolds was investigated. in vitro biological evaluation was examined as well as the apatite formation in simulated body fluid (SBF). The addition of HA particles increased the compressive strength and Young’s modulus of filaments and consequently the scaffolds. Compared to PCL, Young’s modulus of PCL/HA20% filament and three-dimensional (3D) printed scaffold has increased by 30% and 50%, respectively. Also, Young’s modulus for all scaffolds was in the range of 30–70 MPa, which is appropriate to use in spongy bone. Besides, the MTT assay was utilized to evaluate cell viability on the scaffolds. All the samples had qualified cytocompatibility, and it would be anticipated that addition of HA particles raise the biocompatibility in vivo. Alkaline phosphatase (ALP) evaluation shows that the addition of HA caused higher ALP activity in the PCL/HA scaffolds than PCL. Furthermore, calcium deposition in the PCL/HA specimens is higher than control. In conclusion, the addition of HA particles into the PCL matrix, as well as utilizing an inexpensive commercial FFF device, lead to the fabrication of scaffolds with proper mechanical and biological properties for bone tissue engineering applications.