Background This study aimed to assess the effect of irradiation of light-emitting diode (LED) and low-level diode laser on osteogenic/odontogenic differentiation of stem cells from the apical papilla (SCAPs). Materials and Methods SCAPs were isolated from the human tooth root. The experimental groups were subjected to 2–4 J/cm2 diode laser and LED irradiation in osteogenic medium. The control group did not receive any irradiation. Cell proliferation was assessed by the methyl thiazolyl tetrazolium (MTT) assay. Osteogenic differentiation was evaluated by alizarin red staining (ARS), and expression of osteogenic genes by real-time polymerase chain reaction (RT-PCR). Results The MTT assay showed no significant difference in cell viability/proliferation of SCAPs in the laser, LED, and control groups at 24 or 48 hours (P < 0.001). The ARS assessment showed that diode laser and red LED irradiation caused osteogenic differentiation of SCAPs. Diode laser and red LED irradiation both caused over-expression of osteogenic/dentinogenic genes including alkaline phosphatase (ALP), dentin sialophosphoprotein (DSPP), dentin matrix protein 1 (DMP-1), and bone sialoprotein (BSP) in SCAPs. Up-regulation of genes was significantly greater in diode laser irradiation group than LED group (P < 0.001). Conclusions Diode laser with 2–4 J/cm2 energy density and LED can cause osteogenic differentiation and proliferation of SCAPs. Further studies are required to assess the mechanism of effect of diode laser and LED.