The aim of this study is to histologically compare effects of blue light-emitting diode (LED) light (400–490 nm) and Ga–Al–As low-level diode laser light (980 nm) on bone regeneration of calvarial critical-sized defects in rats. Thirty Wistar Albino rats were included in the study. The experimental groups were as follows: blue LED light (400–490 nm) group (LED); 980-nm low-level laser light group (LL); and no-treatment, control group (CL). A critical-sized defect of 8 mm was formed on calvaria of rats. Each animal was sacrificed 21 days after defect formation. Calvarias of all rats were dissected and fixated for histological examination. Histomorphometric measurements of total horizontal length of the newly produced bone tissue, total vertical length of the newly produced bone tissue, and diameter of the newly produced longest bone trabecula were performed with a computer program in micrometers. There was a statistically significant increase in the total horizontal length and total vertical length in LL and LED groups compared to that in the CL group (P < 0.05), while there was no statistical difference between LED and LL groups (P > 0.05). A statistically significant difference was observed in the longest bone trabecula and LL groups compared to that in CL (P < 0.05), but not between LED–CL and LED–LL groups (P > 0.05). In conclusion, blue LED light significantly enhances bone regeneration in critical-sized defects when compared with CL group, but does not have a statistically significant effect on bone regeneration when compared with 980-nm low-level laser light.