Background: The role of fat-free mass loss (FFML) in modulating weight regain in individuals with obesity, as well as the potential mechanisms involved, remain inconsistent. Objectives: The aim of this study was to determine if % FFML following weight loss (WL) is a predictor of weight regain and to investigate the association between %FFML and changes in appetite markers. Methods: Seventy individuals with obesity (BMI: 36 ± 4 kg/m²; age: 44 ± 9 y; 29 males) underwent 8 wk of a very low energy diet (550–660 kcal/d), followed by 4 wk of gradual refeeding and weight stabilization and a 9-mo maintenance program (eucaloric diet). The primary outcomes were body weight and body composition (fat mass and fat-free mass). The secondary outcomes were plasma concentrations of β-hydroxybutyrate (a marker of ketosis) in fasting and appetite-related hormones (ghrelin, glucagon-like peptide 1, peptide YY, and cholecystokinin) and subjective appetite feelings during fasting and every 30 min after a fixed breakfast for 2.5 h. All were measured at baseline, week 9, and 1 y [week 13 in 35 subjects (25 males)]. The association between FFML, weight regain, and changes in appetite was assessed by linear regression. Results: WL at week 9 was 17.5 ± 4.3kg and %FFML 20.4 ± 10.6%. Weight regain at 1 y was 1.7 ± 8.2 kg (8.8 ± 45.0%). After adjusting for WL and fat mass at baseline, %FFML at week 9 was not a significant predictor of weight regain. Similar results were seen at week 13. The greater the %FFML at week 9, but not 13, the smaller the reduction, or greater the increase in basal ghrelin concentration (β: −3.2; 95% CI: −5.0, −1.1; P = 0.003), even after adjusting for WL and β-hydroxybutyrate. Conclusions: %FFML was not a significant predictor of weight regain at 1 y in individuals with obesity. However, a greater %FFML was accompanied by a greater increase in ghrelin secretion under ketogenic conditions, suggesting a link between fat-free mass and appetite regulation. This trial was registered at clinicaltrials.gov as NCT01834859.