The success of tissue-engineering therapies is dependent on the ability of scaffolds to guide differentiation of progenitor cells. Here we present a new approach using a biomimetic construct composed of hydroxyapatite modified with an in vitro-derived extracellular matrix (HA-ECM) and seeded with periodontal ligament progenitor cells (PDLCs). The study aimed to investigate the effect of HA-ECM on osteogenic differentiation of PDLCs and in vivo evaluation of the PDLC-seeded HA-ECM constructs using a rat calvarial critical-sized defect model. After flow-cytometric phenotyping of PDLCs for typical mesenchymal stem cell markers, the PDLCs were cultured on HA-ECM or HA alone in osteogenic media and assessed by MTT, alkaline phosphatase (ALP) assays, and real-time qPCR at different time intervals after seeding. New bone formation induced by PDLC-seeded constructs was assessed by histomorphometric analysis at 12 weeks post-operatively. The PDLCs seeded on HA-ECM showed significantly higher ALP activity and up-regulation of bone-related genes. The treatment with PDLC-seeded HA-ECM significantly improved calvarial bone repair, with the highest amount of newly formed bone elicited by cell-seeded constructs cultured for 14 days. Our results highlight the PDLC-seeded HA-ECM constructs as a promising tool for craniofacial bone regeneration.