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Background: The important risk factors in obesity are related to unhealthy nutritional habits. The aim of this study was to estimate and compare the macro- and micro-nutrients’ intake in breakfast and midmorning snacks. Methods: This cross-sectional study was conducted among 569 students (12-16 years) by the multistage cluster sampling method. The demographic data were gathered by interview. Anthropometric data and breakfast habits (breakfast frequency and time as well as nutrients’ intake at breakfast or snacks) were measured using standardized instruments by asking some questions. Results: The results showed that the high prevalence of irregular breakfast eating (IRBE) and overweight or obesity. No significant difference was found between breakfast frequency and time according to the students’ gender or body mass index (BMI). The mean BMI had a significant increase in females; whereas, the percentage of energy from breakfast (EB%), snack (ES%), or both breakfast and snacks (EBS%) were shown no significant difference between genders. A significant increase was found in EB%, EB%, and EBS%; whereas, the daily energy intake (DEI) was lower in normal-weight students. However, other nutrients at breakfast or snacks had no significant difference. The level of higher DEI was reported in IRBE adolescents. Conclusions: An inappropriate breakfast habit can cause irreparable consequences in adolescents. Although breakfast plays an undeniable role, other factors are also effective in one’s health. Further studies are required for more comprehensive results.