Purpose Corticotomy is an integral part of the Ilizarov method on management of infected nonunited fractures that are challenging orthopaedic surgeons. However, the presence of active draining sinuses may contaminate the operative field with the potential of developing corticotomy site infection. The authors present a surgical technique aiming at minimizing or avoiding the risk of surgical site infection (SSI) in the corticotomy zone. Patients and methods A total of 144 cases of draining infected nonunions were treated by Ilizarov fixator using the corticotomy-first technique. The study included humeral (18 cases), femoral (52 cases), and tibial (74 cases) nonunions. The mean age was 44.48 years with 87 males and 57 females. The mean duration of nonunion was 28.69 months. After debridement, the combined shortening and nonunion gap averaged 5.98 (range 3–10) cm. Evaluation of bone and functional results was done according to Association for the Study and Application of the Method of Ilizarov (ASAMI) criteria. Results The follow-up period averaged 51.05 (range 36–72) months. None of the cases developed corticotomy site or distraction gap infection. Union was successfully achieved in 141 cases (97.92%). Nonunion persisted in three cases (2.08%) in the distal tibia. Infection was eventually controlled in 138 cases (95.83%). Bone grafting was not needed in any case. Conclusions The Ilizarov fixator with the corticotomy-first technique was effective in the management of draining infected non-united fractures of long bones while avoiding the SSI in the corticotomy site in all cases.