Hidradenitis suppurativa (HS) is an uncommon chronic inflammatory disease in children, characterized by painful abscesses and lesions. It has been associated with various autoimmune conditions, including inflammatory bowel diseases (IBDs) and rheumatologic disorders. We present a 13-year-old female with Hurley stage III HS, who developed macrophage activation syndrome (MAS). Clinical presentation and laboratory findings led to a diagnosis of systemic lupus erythematosus (SLE). Treatment with immunosuppressive therapy resulted in symptom resolution and clinical improvement. In addition, a case-based review was conducted to evaluate the patterns, clinical features and possible underlying mechanisms in the pediatric patients with HS and autoimmune diseases. Twenty pediatric cases were included with a median HS onset age of 15 years (IQR: 4 years). Among these, 55% were diagnosed with IBDs, followed by autoimmune arthritis and psoriasis (10% each). Treatment was individualized, with 95% receiving biologic agent and 55% receiving antimicrobials. This case and case-based review of literature highlight the potential overlap between HS and autoimmunity, especially SLE, in the pediatric population and emphasize the importance of proactive monitoring for coexisting autoimmune diseases in patients with HS, in order to facilitate early detection and effective management.