Multimorbidity in pediatrics, defined as the coexistence of at least two chronic diseases or developmental disorders in a single patient, poses an increasing clinical, diagnostic, and therapeutic challenge. This phenomenon is associated with medical advancements that enable the survival of children with severe diseases, but at the same time increase the risk of organ damage and adverse effects of long-term treatment. This manuscript presents the case of a 16-year-old boy who had dilated cardiomyopathy since birth, treated with a heart transplant in early childhood, chronic kidney disease, recurrent gingivitis, short stature, delayed puberty, and iatrogenic Cushing’s syndrome. The patient was diagnosed for short stature and delayed puberty. His medical history has revealed long-term, cyclical use of topical hydrocortisone on the oral mucosa due to recurrent gingivitis following the initiation of immunosuppressive therapy. Physical examination revealed Cushingoid features, abnormal fat distribution, delayed sexual development, and significant bone age delay. Laboratory tests revealed decreased morning cortisol levels, partially preserved adrenal reserve in the Synacthen test, and normal growth hormone secretions in the glucagon stimulation test. The overall clinical picture indicated iatrogenic Cushing’s syndrome with secondary suppression of the hypothalamic-pituitary-adrenal axis. An attempt was made to discontinue hydrocortisone, further endocrinological evaluation was planned, and prophylactic steroid supplementation was recommended for stressful situations. This case demonstrates that even topically applied glucocorticosteroids can lead to serious systemic complications, especially in children with multimorbidity, which justifies the need for close therapeutic monitoring and coordinated multidisciplinary care.