Background: Periodontal diseases lead to bone loss, crestal defects and even loss of the tooth, which also further makes it difficult to replace the tooth. Autogenous bone grafts are considered the gold standard in bone regenerative procedures. This study aimed to compare and evaluate the bone regenerative effects of i-PRF (Injectable- Platelet-rich fibrin) with a bone graft and a bone graft alone in mandibular grade II furcation defects over a period of 9 months. Method: This was a comparative study of 12 participants, who were randomly selected and grouped into two groups: test and control. Following phase I therapy, both groups were subjected to open flap debridement. In the test group, after debridement, a nano-hydroxyapatite bone graft mixed with i-PRF was inserted, whereas in the control group only a nano-hydroxyapatite bone graft was inserted. The clinical parameters such as plaque index (PI), gingival index (GI), pocket probing depth (PPD), clinical attachment level (CAL), horizontal probing depth (HPD) and vertical probing depth (VPD) were recorded at baseline, 3 months, 6 months and 9 months following the surgery. The bone area fill (BAF) was assessed using intraoral periapical radiographs (IOPARs) taken at baseline and 9 months after surgery. Results: At the baseline, there was no statistically significant difference between the tested parameters. After 9 months all the clinical parameters, PI, GI, PPD, CAL, HPD and VPD as well as radiographic bone fill showed a significant increase in both the groups (p < 0.05) (PI-TGr; CGr–VPD—3.5 ± 0.54 to 0.66 ± 0.51; 3.3 ± 0.81 to 2 ± 0.63/BAF—2.9 ± 0.88 to 5.6 ± 1.10; 3.4 ± 1.39 to 3.9 ± 1.4). On comparison the test group showed better results for each clinical parameter. Conclusion: The results showed increased improvement in clinical conditions in both groups, although better results were seen in the group where i-PRF with a nano-HA bone graft was used in the furcation defect.