Background: Congenital junctional epidermolysis bullosa (CJEB) is a rare inherited blistering disorder caused by defects in dermal–epidermal adhesion, resulting in marked skin and mucosal fragility. Although primarily considered a cutaneous disease, CJEB may also cause significant extracutaneous morbidity requiring multidisciplinary care.

Case Presentation: We report a 14-year-old Bahraini male with CJEB and progressive multisystem involvement. Cutaneous manifestations began in early infancy with recurrent rash, nail dystrophy, and secondary infection. Over time, he developed severe airway disease with laryngeal stenosis requiring emergency tracheostomy and subsequent airway interventions. He also experienced progressive cicatrizing ocular surface disease with recurrent symblepharon, conjunctival fibrovascular overgrowth, corneal scarring, and eventual corneal melt requiring multiple reconstructive ophthalmic procedures. In late childhood, genitourinary involvement emerged with penile inflammation, meatal narrowing, urinary retention, and recurrent urethral stricture requiring repeated dilatations and meatotomy.

Management and Outcome: Management was supportive and multidisciplinary, involving dermatology, otolaryngology, ophthalmology, pediatrics, and urology. Interventions included tracheostomy care, laryngeal surgery, repeated ocular surface reconstruction with amniotic membrane transplantation and mitomycin C, catheterization, urethral dilatation, meatotomy, infection treatment, wound care, and long-term surveillance.

Conclusion: This case highlights the severe multisystem burden of CJEB and emphasizes that it is not solely a skin disorder. Early recognition of extracutaneous complications, close follow-up, and coordinated multidisciplinary management are essential to reduce morbidity and preserve function and quality of life.