Background and Objectives: We analyzed the changes in obesity, glucose metabolism, and body composition over a 3-year period in Japanese patients with obesity following laparoscopic sleeve gastrectomy (LSG). Methods: Body weight, parameters related to diabetes such as glycated hemoglobin (HbA1c), and electrical impedance analysis were used to assess body composition in forty-eight Japanese patients with obesity before surgery and 6 months, 1 year, 2 years, and 3 years after LSG. Results: At 6 months, 1, 2, and 3 years post-LSG, there were significant reductions in body weight, body mass index, blood pressure, fasting plasma glucose, triglyceride, and HbA1c levels. Six months after LSG, fat mass (FM), muscle mass (MM), and %FM all showed a decrease compared to pre-treatment values (all p < 0.05). FM and %FM remained in a decreased state until 3 years had passed. In contrast, %MM increased at 6 months post-LSG and was maintained up to 3 years post-LSG (all p < 0.05). Furthermore, changes in FM and %FM were associated with changes in body weight and A1C. In contrast, change in %MM exhibited a negative correlation with body weight and A1C following LSG. Finally, multivariate regression analyses demonstrated that alterations in FM were independent factors affecting body weight in patients with obesity 3 years after LSG. Conclusions: We observed improvements in FM, fasting plasma glucose, and HbA1c levels over a 3-year period in Japanese patients after LSG. The reduction in FM and maintenance of %MM after LSG were suggested as possible links between the effects of LSG on obesity and diabetes over 3 years.