This study examined differences in breakfast habits, mental health, and the prevalence of allergic diseases among 9,549 adolescents from father-headed and mother-headed families, using raw data from the 2017~2019 Korea Youth Risk Behavior Web-Based Survey. Of the total participants, 44.6% came from father-headed families, while 55.4% were from mother-headed families. Single-parent adolescents showed the highest likelihood of eating breakfast every day of the week (24.5%), but they also had a significant tendency to skip breakfast entirely (24.3%). There was no significant difference in breakfast frequency between those from father-headed and mother-headed families. The perception of stress and subjective health status did not differ significantly between adolescents from the two types of families, although subjective health status did show significant differences among boys. Depressive experiences were notably higher in adolescents from mother-headed families (33.0%) compared to those from father-headed families (30.8%). Additionally, the prevalence of atopic dermatitis and allergic rhinitis was significantly greater in adolescents from mother-headed families (24.2% and 32.1%, respectively) than in those from father-headed families (21.1% and 26.5%, respectively). These results indicate the need for tailored nutrition and health guidance programs for adolescents from single-parent families to support the role of the absent parent.