Abstract Background Management of atypical femoral fracture on bisphosphonate therapy still remains controversy and is reported high rate of complications. The aim of this study was to evaluate the outcome of intramedullary nailing in patients with atypical femoral fracture who took bisphosphonate more than one year through the multicenter retrospective study. Methods We gathered 75 atypical femoral fractures from seven institutions between 2009 and 2014. Among them 46 atypical femoral fractures which met the inclusion criteria was evaluated in this study. The average age was 70.1 years (53 to 80) and the average duration of bisphosphonate use was 5.1 years (1 to 15 years). Medical records and radiographs were reviewed to determine time to union, union rate, need for revision surgery, restoration of ambulatory function, and complications. Results Twenty-nine (63%) fractures healed within 6 months without complications. The average time to union except two non-union was 24.9 weeks (11 to 48 weeks). Two patients (4.3%) underwent revision surgery for non-union and there was no implant failure. Thirty-seven (80.4%) patients achieved their pre-fracture ambulatory function at the final follow up. Conclusions Although the incidence of delayed bone healing is high in atypical femoral fracture on bisphosphonate therapy even treated with intramedullary nailing, the incidence of revision surgery and implant failure was relatively lower than those of extramedullary devices.