The demand for bone grafting procedures in various fields of medicine is increasing. Existing substitutes in clinical practice do not meet all the criteria required for an ideal bone scaffold, so new materials are being sought. This study evaluated bone regeneration using a critical-size Wistar rat’s calvarial defect model. 12 male and 12 female rats were evenly divided into 3 groups: 1. Negative and positive (Geistlich Bio-Oss®) controls; 2. polylactic acid (PLA) and PLA/hydroxyapatite (HA); 3. PLA/HA cellularised with dental pulp stem cells (DPSC) and PLA/HA extracellular matrix (ECM) scaffolds. PLA/HA filament was created using hot-melt extrusion equipment. All scaffolds were fabricated using a 3D printer. DPSC were isolated from the incisors of adult Wistar rats. The defects were evaluated by micro-computed tomography (µCT) and histology, 8 weeks after surgery. µCT revealed that the Bio-Oss group generated 1.49 mm3 and PLA/HA ECM 1.495 mm3 more bone volume than the negative control. Histology showed a statistically significant difference between negative control and both (Bio-Oss and PLA/HA ECM) groups in rats of both genders. Moreover, histology showed gender-specific differences in all experimental groups and a statistically significant difference between cellularised PLA/HA and PLA/HA ECM groups in female rats. Qualitative histology showed the pronounced inflammation reaction during biodegradation in the PLA group. In conclusion, the bone-forming ability was comparable between the Bio-Oss and PLA/HA ECM scaffolds. Further research is needed to analyse the effects of ECM and PLA/HA ratio on osteoregeneration.