This study was conducted in order to investigate biological compatibility of a thin and flexible hydroxyapatite (HAP) paper which consists of ultralong hydroxyapatite nanowires. Circular-shaped cranial bone defects with a diameter of 8.8 mm were prepared to expose the dura maters in Wistar rats. The similar-sized, circular-shaped HAP paper was placed at the bottom of the bone defects. After 2, 4, and 8 weeks, the rats were sacrificed, and the experimental sections were examined by micro-CT scanning and histological observation. The HAP paper covered with fibrous tissues showed no inflammatory cell infiltration, and their thicknesses decreased over time. Tartrate-resistant acid phosphatase-positive osteoclast-like cells were induced around the edges of the HAP paper along with the exfoliation of the HAP paper. The newly-formed bones were observed in the bone-defected areas, either with a direct contact with the HAP paper or through thin fibrous tissues. The HAP paper-induced osteoblast differentiation was confirmed since the alkaline phosphatase activities were detected on the surfaces of the HAP paper. These results indicated that the HAP paper may induce osteogenesis without causing any harmful effects. The highly flexible HAP paper can contribute to further development of bone regenerative therapy.