There have been no studies comparing the outcomes of nonvascularized autograft (NA) and allograft after resection of primary bone tumors. This study compares the clinical, functional outcomes of NA and allograft reconstruction and analyzes the risk factors for failure after these procedures. A retrospective study of patients with primary bone tumors of the extremities who underwent NA (n = 50) and allograft reconstruction (n = 47). The minimum follow up time was 24 months. The mean time to union for the NA and allograft group was 9.8 ± 2.9 months and 11.5 ± 2.8 months, respectively (p = 0.002). Reconstruction failure in the NA and allograft group was 19 (38%) and 26 (55.3%), respectively. Nonunion (30%) was the most common complication found in the NA group, while structural failure (29.8%) was the most common in the allograft group. There was no significant difference in functional outcome in terms of the mean Musculoskeletal Tumor Society score between the NA and allograft groups (23.5 ± 2.8 and 23.9 ± 2.1, respectively, p = 0.42). Age, sex, tumor location, graft length, method of reconstruction did not significantly influence failure of reconstruction. Chemotherapy was the only significant risk factor affecting outcomes (HR = 3.49, 95% CI = 1.59–7.63, p = 0.002). In the subgroup analysis, the use of chemotherapy affected graft-host nonunion (p < 0.001) and structural failure in both the NA and allograft groups (p = 0.02). Both NA and allograft reconstruction methods provide acceptable clinical and functional outcomes. Chemotherapy is a risk factor for failure of both reconstructions, particularly graft-host nonunion and structural failure.