The purpose of this study was to assess the success rate and functional outcomes of bone grafting for periprosthetic bone cysts following total ankle arthroplasty (TAA). Additionally, we evaluated the rate of graft incorporation and identified associated predisposing factors using CT scan. We reviewed a total of 37 ankles (34 patients) that had undergone bone grafting for periprosthetic bone cysts. A CT scan was performed one year after bone grafting to check the status of graft incorporation. For accurate analysis of cyst volumes and their postoperative changes, 3D-reconstructed CT scan processed with 3D software was used. For functional outcomes, variables such as the Ankle Osteoarthritis Scale score and the visual analogue scale for pain were measured. Out of 37 ankles, graft incorporation was successful in 30 cases. Among the remaining seven cases, four (10.8%) exhibited cyst re-progression, so secondary bone grafting was needed. After secondary bone grafting, no further progression has been noted, resulting in an overall 91.9% success rate (34 of 37) at a mean follow-up period of 47.5 months (24 to 120). The remaining three cases (8.1%) showed implant loosening, so tibiotalocalcaneal arthrodesis was performed. Functional outcomes were also improved after bone grafting in all variables at the latest follow-up (p < 0.05). The mean incorporation rate of the grafts according to the location of the cysts was 84.8% (55.2% to 96.1%) at the medial malleolus, 65.1% (27.6% to 97.1%) at the tibia, and 81.2% (42.8% to 98.7%) at the talus. Smoking was identified as a significant predisposing factor adversely affecting graft incorporation (p = 0.001). Bone grafting for periprosthetic bone cysts following primary TAA is a reliable procedure with a satisfactory success rate and functional outcomes. Regular follow-up, including CT scan, is important for the detection of cyst re-progression to prevent implant loosening after bone grafting.