Spinal cord injury (SCI) is associated with an increased risk of nephrolithiasis. We performed a systematic review and meta-analysis to assess stone clearance and complication rates following surgical treatment of kidney stones in this population. We systematically reviewed the Ovid MEDLINE, Embase, CENTRAL, and Web of Science databases for studies examining outcomes of kidney stone procedures in SCI patients. Our primary outcomes were stone-free rate (SFR) and complications, as categorized by Clavien-Dindo classification. A meta-analysis of comparative studies was performed to assess differences in outcomes between SCI and non-SCI patients following PCNL. A total of 27 retrospective and observational articles were included. Interventions for kidney stones included PCNL, shockwave lithotripsy (SWL), and ureteroscopy. Pooled SFR in SCI patients undergoing surgery for kidney stones was 54.1%, for SWL, 73.6% for PCNL, and 36.2% for ureteroscopy. Four studies compared outcomes following PCNL in SCI and non-SCI patients. Meta-analysis found that there were higher rate of grades I (OR 9.54; 95% CI, 3.06-29.79), II (OR 3.38; 95% CI, 1.85-6.18), and III-V (OR 2.38; 95% CI, 1.35-4.19) complications in SCI patients compared to non-SCI patients following PCNL. The rate of infectious complications was also higher in patients with SCI (OR 6.15; 95% CI, 1.86-20.39). However, there was no difference in SFR (OR 0.64; 95% CI, 0.15-2.64) between groups. Patients with SCI are at higher risk of complications following PCNL compared to non-SCI patients. SFR after PCNL was equivalent between groups, suggesting that PCNL is an effective surgery for kidney stones in SCI patients.