This study aimed at exploring atopic dermatitis (AD) prevalence in children and exhaustively analyzing their comorbidity. We conducted a descriptive analysis of their socio-demographic and comorbidity characteristics in the EpiChron Cohort (Aragón, Spain). Adjusted odds ratios (OR) were calculated for each comorbidity using logistic regression models. In total, 33,591 children had a diagnosis of AD, resulting in an overall prevalence of 15.5%. AD prevalence was higher in girls compared to boys, in 3–9-year-olds compared to children of other ages, and in Spanish children compared to those of other nationalities. Multimorbidity was present in 43% of children, with the most frequent chronic comorbidities being asthma (13.1%), psychosocial disorders (7.9%), and visual impairment (7.8%). Many diseases were, regardless of their prevalence, statistically associated with AD. The strongest associations (odds ratio (OR) (95% confidence interval (CI))) were found in asthma (2.10 (2.02–2.17)), allergic rhinitis (2.00 (1.91–2.10)), and irritable bowel syndrome (1.90 (1.56–2.31)). A better understanding of the array of comorbidities associated with AD in children might help improve their clinical management. Future longitudinal studies are encouraged to shed light on the potential underlying pathophysiological mechanisms involved in the identified associations.