Obesity is a global health concern linked to metabolic and cardiovascular complications. Bariatric surgery is an effective treatment, with sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (RYGB) being the most studied procedures. This systematic review and meta-analysis compare the long-term efficacy and safety of SG and RYGB. We searched PubMed, Embase, and the Cochrane Library until May 20, 2024, for randomized trials with ≥ 5 years of follow-up comparing SG and RYGB. Primary outcomes included excess weight loss (EWL), total weight loss (TWL), and excess BMI loss (EBL). Secondary outcomes included diabetes remission, HbA1c levels, obesity-related comorbidities, complications, and mortality. Risk ratios (RRs) and mean differences (MDs) with 95% confidence intervals (CIs) were pooled using a random-effects model. We included 9 randomized trials encompassing 1,489 patients. RYGB resulted in significantly greater EWL (MD -14.00%; 95% CI -20.65 to -7.35), TWL (MD -5.67%; 95% CI -8.81 to -2.52), and EBL (MD -7.44%; 95% CI -10.54 to -4.34) compared to SG. T2DM remission was higher in the RYGB group (RR 0.72; 95% CI 0.54-0.97), although HbA1c levels were similar between groups. RYGB also led to greater improvement in GERD symptoms (RR 0.48; 95% CI 0.31-0.74). No significant differences were observed between SG and RYGB in dyslipidemia, hypertension, obstructive sleep apnea syndrome (OSAS), or joint pain. Regarding safety, SG was associated with significantly lower late major complications (RR 0.41; 95% CI 0.20-0.85), while early minor (RR 0.55; 95% CI 0.17-1.83), early major (RR 0.99; 95% CI 0.45-2.20), and late minor complications (RR 0.77; 95% CI 0.39-1.54) did not differ significantly between procedures. Only one surgery-related death was reported, occurring in the early postoperative period in the SM-BOSS trial. RYGB is associated with greater long-term weight loss, improved T2DM remission, and superior GERD control compared to SG. However, SG showed a lower incidence of late major complications. Both procedures were comparable for the remaining outcomes. These findings highlight the importance of considering both efficacy and safety in the context of individual patient characteristics, rather than focusing solely on weight loss.