Protein plays a crucial role in the growth and development of adolescents. However, being a secondary energy source, protein’s role in obesity has been sidelined. We examined whether intake of protein (total, animal, plant), branched-chain (BCAAs), and sulfur-containing (SCAAs) amino acids are associated with general body and central obesity and body composition in a cross-sectional study among healthy adolescents. Students aged 12–18 years old (n = 601) in schools near two major Adventist universities in California and Michigan provided dietary data via a validated web-based food frequency questionnaire (FFQ) and anthropometric data during school visits. Intakes of total, animal, and plant proteins, and BCAAs and SCAAs were derived from FFQ data. We defined general body obesity with body-mass-index-for-age (BMIz) z-scores and central obesity with waist-to-height ratios (WHtR). After full adjustment for covariates, multiple regression analyses showed significant positive associations between intakes of total protein (β = 0.101, 95% CI: 0.041, 0.161), animal protein (β = 0.118, 95% CI: 0.057, 0.178), BCAAs (β = 0.056, 95% CI: 0.025, 0.087), and SCAAs (β = 0.025, 95% CI: 0.012, 0.038) with general body adiposity. Animal protein (β = 0.017, 95% CI: 0.001, 0.033) and SCAAs (β = 0.004, 95% CI: 0.000, 0.008) were also associated with central obesity. Total and animal protein and BCAA and SCAA were also significantly associated with fat mass. Our findings suggest that high protein intake may pose a possible detriment to adolescent health. Longitudinal and safety evaluation studies are recommended.