Hydroxyapatite/collagen (HAP/Col) composite has a nanostructure and composition similar to that of natural bone. Herein, we have evaluated the beneficial effects of acid‐electrolyzed functional water (FW) in combination with HAP/Col composite as an irrigation material in a rat calvarium defect model. The rats were divided into four groups: control, PBS irrigation; FW, FW irrigation; HAP/Col, filled with HAP/Col; FW + HAP/Col, FW irrigation prior to HAP/Col filling. Bone volume (BV) and bone mineral density (BMD) of the newly formed bone were analyzed by microcomputed tomography. The results indicated that the combined use of FW and HAP/Col significantly augmented both BV (12.25 ± 1.93 mm3, control: 3.22 ± 0.55 mm3, 6 weeks) and BMD (120.09 ± 14.76 cm3/mg vs. control: 54.67 ± 7.20 cm3/mg, 6 weeks) in a time‐dependent manner, which might be attributed to the soluble factor‐inducing ability of FW. Based on this assumption, bFGF concentration in peripheral blood was measured. bFGF concentration was significantly increased in the FW + HAP/Col group (68.25 ± 9.2 pg/ml vs. control: 21.70 ± 8.18 pg/ml, 6 hr). Real‐time PCR demonstrated significant augmentation of MCSF (2.82 ± 0.59‐fold), RANKL (2.51 ± 0.33‐fold) and BMP7 (1.66 ± 0.25‐fold) (bone regeneration‐related genes) and PDGF (1.31 ± 0.15‐fold), VEGF (3.27 ± 0.42‐ld) and IL‐8 (6.77 ± 2.02‐fold) (angiogenic genes) mRNAs in the FW + HAP/Col group. Taken together, these results suggest that the combined use of FW and HAP/Col induces bone regeneration, presumably by inducing the factors contributing to bone regeneration and angiogenesis.