Amputees frequently suffer from chronic pain in both their residual limbs (RLP) and phantom limbs (PLP) following their amputation. Targeted muscle reinnervation (TMR) is a nerve transfer technique that has been demonstrated to improve pain secondarily and at time of amputation. The goal of this study is to report on the efficacy of primary TMR at time of above-knee level amputations in the setting of limb-threatening ischemia or infection. This is a retrospective review of a single-surgeon experience with TMR in patients undergoing through- or above-knee level amputations from January 2018 to June 2021. Patient charts were reviewed for the comorbidities in the Charlson Comorbidity Index. Postoperative notes were assayed for presence and absence of RLP and PLP, overall pain severity, chronic narcotic use, ambulatory status, and complications. A control group of patients undergoing lower limb amputation who did not receive TMR from January 2014 to December 2017 was used for comparison. Forty-one patients with through- or above-knee level amputations and primary TMR were included in this study. The tibial and common peroneal nerves were transferred in all cases to motor branches to the gastrocnemius, semimembranosus, semitendinosus, and biceps femoris. Fifty-eight patients with through- or above-knee level amputations without TMR were included for comparison. The TMR group had significantly less overall pain (41.5 vs. 67.2%, p = 0.01), RLP (26.8 vs. 44.8%, p = 0.04), and PLP (19.5 vs. 43.1%, p = 0.02). There were no significant differences in complication rates. TMR can safely and effectively be performed at time of a through- and above-knee level amputation and improves pain outcomes.