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<b>Background/Objectives</b>: Childhood obesity remains a major global health challenge influenced by poor dietary patterns and excessive energy intake. Understanding gender-specific nutritional deviations may improve the effectiveness of preventive and therapeutic interventions. This study aimed to evaluate differences in energy and nutrient intake between boys and girls with overweight or obesity status and to identify the main food sources contributing to these differences. <b>Methods</b>: Data from a total of 180 participants (83 boys, 97 girls; 7-18 years) attending the national obesity intervention program Camp My Challenge was analyzed. Anthropometric parameters and dietary intake were assessed using a validated food-frequency questionnaire (OPKP). Intakes were compared with Slovenian dietary reference values (DRVs). Group differences were tested using ANOVA, <i>t</i>-tests, and Pearson correlations (<i>p</i> < 0.05). <b>Results</b>: Boys exhibited higher body mass (79.9 ± 22.6 kg vs. 69.2 ± 19.1 kg; <i>p</i> = 0.001) and BMI (30.8 ± 4.8 kg/m<sup>2</sup> vs. 28.5 ± 4.4 kg/m<sup>2</sup>; <i>p</i> = 0.001). Mean energy intake was 2543 ± 1138 kcal/day, exceeding DRV by 16% (t = 3.31, <i>p</i> < 0.001). Girls exceeded energy requirements by 24.5% vs. 5.4% in boys (<i>p</i> = 0.019). Boys consumed significantly more total fat (106 ± 61 g vs. 85 ± 47 g; <i>p</i> = 0.014), saturated fatty acids (34 ± 20 g vs. 27 ± 13 g; <i>p</i> = 0.011), protein (119 ± 63 g vs. 98 ± 41 g; <i>p</i> = 0.008), and sodium (3628 ± 2086 mg vs. 2852 ± 1520 mg; <i>p</i> = 0.005). Girls showed higher sugar intake (208% vs. 166% of DRV; <i>p</i> = 0.032), mainly from sweet foods (24%) and fruit (26%), whereas beverages-predominantly isotonic drinks-accounted for 27% of boys' sugar intake. Sugar intake correlated with waist circumference (r = 0.305, <i>p</i> = 0.002) and fat mass (r = 0.272, <i>p</i> = 0.007) in girls. Sodium intake exceeded DRV sixfold in both sexes. <b>Conclusions</b>: Marked sex-specific dietary disparities exist among children with obesity. Interventions should target high sugar and energy intake in girls and excessive fat, sodium, and sugar-sweetened beverage consumption in boys to enhance the efficacy of pediatric obesity management.