This prospective study compared bifocal acute shortening and relengthening (ASR) with bone transport (BT) in a consecutive series of complex tibial infected non-unions and osteomyelitis, for the reconstruction of segmental defects created at the surgical resection of the infection. Patients with an infected tibial segmental defect (>2 cm) were eligible for inclusion. Patients were allocated to ASR or BT, using a standardized protocol, depending on defect size, the condition of soft tissues and the state of the fibula (intact or divided). We recorded the Weber–Cech classification, previous operations, external fixation time, external fixation index (EFI), follow-up duration, time to union, ASAMI bone and functional scores and complications. A total of 47 patients (ASR: 20 patients, BT: 27 patients) with a median follow-up of 37.9 months (range 16–128) were included. In the ASR group, the mean bone defect size measured 4.0 cm, and the mean frame time was 8.8 months. In the BT group, the mean bone defect size measured 5.9cm, and the mean frame time was 10.3 months. There was no statistically significant difference in the EFI between ASR and BT (2.0 and 1.8 months/cm, respectively) (p = 0.223). A total of 3/20 patients of the ASR and 15/27 of the BT group needed further unplanned surgery during Ilizarov treatment (p = 0.006). Docking site surgery was significantly more frequent in BT; 66.7%, versus ASL; 5.0% (p < 0.0001). The infection eradication rate was 100% in both groups at final follow-up. Final ASAMI functional rating scores and bone scores were similar in both groups. Segmental resection with the Ilizarov method is effective and safe for reconstruction of infected tibial defects, allowing the eradication of infection and high union rates. However, BT demonstrated a higher rate of unplanned surgeries, especially docking site revisions. Acute shortening and relengthening does not reduce the fixator index. Both techniques deliver good functional outcome after completion of treatment.