This study evaluated the comprehensive and sequential gene expression in laser-ablated bone compared with that in nontreated control bone. Bone ablation by Er:YAG laser has shown positive effects on bone healing; however, the gene expression responses that occur during bone healing remain unclear. The calvarial bone of male, 10-week-old Wistar rats was ablated by Er:YAG laser. Gene expression in the laser-ablated bone and nontreated control bone was evaluated at 6, 24, and 72 h using microarray analysis. Messenger RNA (mRNA) expression levels were validated by quantitative reverse transcription-polymerase chain reaction. Gene expression of BCAR1/p130Cas (breast cancer anti-estrogen resistance 1/p130 Crk-associated substrate), a mechanotransducer, was gradually increased. Additionally, upstream of the Hippo signaling pathway was enriched according to Kyoto Encyclopedia of Genes and Genomes pathway analysis at 6 h. F-actin mRNA expression was also gradually increased, whereas the Hippo signaling pathway was downregulated from 6 to 24 h. Enrichment of bone formation-related Gene Ontology (GO) terms was observed from an early stage, whereas inflammation-related GO terms, gene sets, and mRNA expression of , , and were gradually enriched after 24 h. Bone ablation by Er:YAG laser regulated the expression of and , the main regulators of mechanotransduction in the bone tissue. Additionally, inflammation was gradually increased up to 72 h following bone ablation with Er:YAG laser. Laser influences the expression of genes associated with bone formation immediately after irradiation. Therefore, mechanical stress and the biological effects caused by Er:YAG laser irradiation potentially contribute to wound healing in the laser-ablated bone tissue.