Existing evidence examining the relation between egg consumption and metabolic health of overweight/obese adolescents is scarce. We examined the association between egg consumption and metabolic status in Iranian overweight/obese adolescents. Using multistage cluster random sampling approach, overweight/obese adolescents (n = 203) with ages from 12 to 18 years old were selected for the present cross-sectional study. A validated 147-item food frequency questionnaire was adopted to determine usual dietary intakes. Blood pressure and anthropometric data and were assessed, and levels of lipid profile, insulin, and glucose were measured by collecting fasting blood samples. Participants were classified into metabolically healthy obese (MHO) or metabolically unhealthy obese (MUO) based on two methods of International Diabetes Federation (IDF) and the combination of IDF with Homeostasis Model Assessment Insulin Resistance (HOMA-IR). In total, 67 (33.0%) and 79 (38.9%) adolescents were classified as MUO based on IDF/HOMA and IDF definitions, respectively. Considering IDF criteria, the highest intake of egg was related to decreased chance of MUO, in crude (OR 0.22; 95% CI 0.10–0.48) and maximally-adjusted model (OR 0.25; 95% CI 0.10–0.59). Considering IDF/HOMA-IR criteria, similar results were obtained (crude model: OR 0.24; 95% CI 0.11–0.52; fully-adjusted model: OR 0.28; 95% CI 0.11–0.69). Stratified analyses found stronger relation among boys (vs. girls) and overweight (vs. obese) individuals. In conclusion, higher egg consumption was negatively related to decreased chance of being MUO in overweight/obese adolescents, especially in boys and overweight individuals, regardless of MUO definitions. Prospective studies are required to support our results.