The aim was to investigate the possible association of dietary calcium intake with adiposity, insulin resistance, and adipocytokine values in adolescent boys. In this cross-sectional study, participants were 123 adolescent boys aged 13–15 years, who were divided into tertiles according to their dietary calcium intake. Dietary calcium intake was assessed using three 24 h dietary recalls. In addition, energy intake, body composition, physical activity (PA), and blood biochemical values were also measured. Mean body fat%, fat mass (FM), trunk FM, trunk fat%, and leptin differed between high and low tertiles of calcium intake after adjustment for age, pubertal stage, and PA. For the entire cohort, mean calcium intake was 786 ± 380 mg/day and was related to body mass index (BMI), FM, and trunk fat% but not to insulin resistance or adipocytokine values after adjusting for possible confounders. In addition, only 15.4% of the participants obtained or exceeded their mean dietary calcium intake requirements. These subjects who met their dietary calcium intake had significantly lower body fat% in comparison with subjects not meeting their dietary calcium intake. Odds ratio of being in the highest tertile of FM, trunk FM, and trunk fat% was 3.2–4.4 (95% confidence interval 1.19–12.47; p < 0.05) times higher for boys in low calcium intake tertile, compared to those boys in high calcium intake tertile. In conclusion, dietary calcium intake is inversely associated with total body and abdominal adiposity values in a specific group of healthy male adolescents with different body mass values.