Tooth biomaterial may be useful in bone regeneration for restoring peri-implant defects in vivo. The aim of this study was to compare bone regeneration capacity in peri-implant defects augmented with autogenous tooth biomaterial combined with platelet-rich fibrin (PRF), tooth biomaterial alone, or PRF alone. Two monocortical defects were generated on each tibia of 10 New Zealand white rabbits (n = 10 per group) with a trephine bur, and the dental implant was installed into the defects. In experimental groups 1, 2, and 3, the peri-implant defects were filled with tooth biomaterial and platelet-rich fibrin (PRF), tooth biomaterial only, and PRF only, respectively and the control was left empty. Micro computed tomography (CT), implant stability, and histomorphometric analysis were conducted eight weeks after operation. The mean regenerated bone areas were 53.87 ± 7.60%, 51.56 ± 6.45%, and 18.45 ± 1.34% in experimental groups 1, 2, and 3, respectively, and 11.57 ± 1.12% in the control. Mean bone-to-implant contact values were 43.67 ± 2.50%, 41.07 ± 2.59%, and 21.45 ± 1.25% in experimental groups 1, 2, and 3, respectively, and 16.57 ± 2.83% in the control. Tooth biomaterial enriched with platelet-rich fibrin (PRF) and tooth biomaterial alone showed more enhanced regeneration than PRF alone in our study.