Chronic pain remains a significant challenge for individuals following limb amputation, with incidence of painful neuromas, phantom limb pain (PLP), and residual limb pain (RLP). Targeted muscle reinnervation (TMR) is a surgical technique designed to restore motor control information lost during amputation by redirecting residual nerves to new muscle targets. This systematic review and meta-analysis aims to compare patient-reported and functional outcomes following amputation with either TMR or standard neurological treatment (SNT). The study also includes an examination of primary versus secondary TMR and explores outcomes in highly comorbid patient populations. A search of central databases was performed, and meta-analysis was completed on extracted data where possible. Eleven studies were identified. Results indicate a significant reduction in PLP and RLP in patients undergoing TMR compared to SNT using various pain scores. TMR also demonstrates improved functional outcomes and decreased opioid use. Furthermore, results indicated patients who underwent TMR at the time of amputation (primary TMR) had improved pain scores compared with those who had TMR performed later (secondary TMR). The review emphasizes the benefits of TMR as a valuable surgical adjunct for amputee patients, while also highlighting the need for further research, especially in comorbid populations.