(1)Human periodontal ligament stem cells (HPDLSCs) are a unique population of mesenchymal stem cells (MSCs). Recently, the positive effects of photobiomodulation on the regulation of MSCs proliferation and osteogenic differentiation have gained significant attention. This study aimed to assess the effects of photobiomodulation and vitamin D (as an anabolic factor) on HPDLSCs for bone regeneration. (2)HPDLSCs were collected, isolated, and characterized and then divided into six groups: groups I and II, control and (10-7 Mol) vitamin D, respectively; group III, irradiation at 1 J/cm2 of 808-nm diode laser; group IV, irradiation at 1 J/cm2 and culture with vitamin D; group V, irradiation at 2 J/cm2, and group VI, irradiation at 2 J/cm2 and culture with vitamin D. Cell viability assay was measured through MTT assay and cell growth curve. Alkaline phosphatase (ALP) enzyme activity and mRNA levels of RUNX2, collagen 1 (Col-1), ALP, and osteonectin were also assessed. (3)Photobiomodulation at 1 and 2 J/cm2 combined with vitamin D significantly promoted HPDLSC proliferation (in MTT assay and cell growth curve results) and osteogenic differentiation (through the gene expression of RUNX2, Col-1, ALP, and osteonectin levels (p < 0.05). (4)Laser irradiation at 2 J/cm2 combined with vitamin D3 enhanced osteoblast differentiation and proliferation of cultured HPDLSCs and thus could further substitute bone grafting.