This study aimed to compare the efficacy of allogeneic stem cell transplantation (allo-SCT) versus autologous SCT (auto-SCT) in patients with relapsed or refractory B-cell non-Hodgkin lymphoma (B-NHL). Medline, CENTRAL, and EMBASE databases through December 31, 2019 were searched. The primary endpoints were overall survival (OS) and progression-free survival (PFS) rates. The secondary outcomes include transplant-related mortality (TRM), event-free survival, relapse/or progression, and nonrelapse mortality (NRM). The 18 retrospective studies enrolled 8,058 B-NHL patients (allo-SCT = 1,204; auto-SCT = 6,854). The OS was significantly higher in patients receiving auto-SCT than allo-SCT (pooled odds ratio [OR]: 1.69, 95% confidence interval [CI]: 1.29 to 2.22, < 0.001), but no significant difference was found in PFS (pooled OR: 0.98, 95% CI: 0.69 to 1.38, = 0.891). Auto-SCT patients also had lower TRM and NRM (TRM: OR = 0.23, < 0.001; NRM: OR = 0.16, < 0.001), but higher relapse or progression rate (OR = 2.37, < 0.001) than allo-SCT patients. Subgroup analysis performed for different grades and subtypes of B-NHL showed higher OS in auto-SCT patients with high-grade B-NHL and diffused large B-cell lymphoma (DLBCL). There was, nevertheless, higher PFS in allo-SCT patients with low-grade B-NHL and follicular lymphoma (FL), and lower PFS in allo-SCT patients with DLBCL than their auto-SCT counterparts. In conclusion, the meta-analysis demonstrated that relapsed or refractory B-NHL patients who received auto-SCT have improved OS than those treated with allo-SCT, especially among those with DLBCL, but lower PFS among those with FL. However, the study is limited by a lack of randomized trials, patients' heterogeneity, and possible selection bias.