The effect of bariatric surgery on resting energy expenditure (REE) remains unclear, particularly in terms of the REE/fat-free mass (FFM) ratio. We performed a systematic review with a meta-analysis on Roux-en-Y gastric bypass (RYGB) studies to investigate the effect of bariatric surgery on the REE/FFM ratio 6 and 12 months postoperatively. Five of the 13 records of 6-month data (n = 406) showed a reduction in the REE/FFM ratio without significant summary effects. As regards 12-month data (10 records, n = 713), there was a significant relative REE mean reduction of 1.95 kcal/kg in FFM (CI: -2.82 to -1.09; I2 = 28%; p < 0.00001). These findings suggest that bariatric surgery, specifically RYGB, leads to a decrease in the REE/FFM ratio during the first postoperative year, which may compromise long-term treatment outcomes.