We conducted this study to evaluate the use of rail fixation system in infected gap non-union of femur and tibia as an alternative to the established Ilizarov circular fixator technique. Prospective study. The study was done in the Department of Orthopaedic surgery in a medical school and level I trauma center to which the authors are/were affiliated. Between June 2010 and June 2015, 40 patients with infected gap non-union of femur and tibia were treated with the rail fixation system. Patients who were willing to undergo surgery and participate in the post-operative rehabilitation were included in the study. After radical debridement, the system was applied and corticotomy done. For closure of bone gap, acute docking and distraction was done in 18 cases and segmental bone transport in 22 cases. Early mobilization of patient was done along with aggressive physiotherapy. Bone and functional results were calculated according to ASAMI scoring system, and complications were classified according to Paley classification. The mean follow-up period was 22.56 months (range 8-44). Bone union with eradication of infection was achieved in all but 1 case (97.5%). Bone results were excellent in 57.5%, good 40%, fair 0% and poor in 2.5% cases, while functional result was excellent in 32.5%, good 65%, fair 0% and poor in 2.5% cases. The rail fixation system is an excellent alternative method to treat infected gap non-union of femur and tibia. It is simple, easy to use and patient-friendly.