Abstract Objectives To assess whether Bone transport through induced membrane (BTM) has better outcomes regarding docking site union and infection recurrence than conventional bone transport (BT) or not in the treatment of infected lower limb long bones defects. Methods A prospective randomized controlled study in a single institution was conducted. A total of 30 patients with infected non united fractures of long bones of lower limbs were divided into 15 patients (10 femurs, 5 tibias) treated by BTM and 15 patients (3 femurs,12 tibias) treated by BT. The outcome measures includes external fixation time (EFT), external fixation index (EFI), docking time (DT), bone and functional outcomes evaluated by the Association for the Study and Application of the Method of Ilizarov (ASAMI) scoring system, postoperative complications evaluated by Paley classification and number of additional operations. Results The mean docking time (DT) was significantly lower in BTM group in comparison to BT group (3.67 ± 0.82 months vs 4.80 ± 0.86 months respectively) (p value 0.001). Docking site nonunion and infection recurrence were significantly lower in BTM group in comparison to BT group (0% vs 40% respectively) (p value 0.02) and (0% vs 33.3% respectively) (p value 0.04). Mean number of additional operations per patient was significantly lower in BTM group in comparison to BT group (0 vs 0.80 ± 1.08 operations respectively) (p value 0.01) Conclusion Both BTM and BT achieved satisfactory postoperative bone and functional outcomes in patients with infected long bones defects of lower limbs, while BTM had significantly faster docking site union, lower incidence of postoperative complications including docking site nonunion and infection recurrence rates and lower number of additional operations needed at the expense of 2 staged procedure in comparison to BT.