Background Inherited epidermolysis bullosa (EB) is a rare group of monogenic disorders causing skin fragility. Junctional EB is the rarest subtype, caused by mutations in genes like COL17A1. Type 1 diabetes mellitus (DM) is a polygenic autoimmune disease. The co‐occurrence of a primary structural genetic defect and a systemic autoimmune disorder is rare. This case represents a second rare co‐occurrence of EB and type 1 DM in a pediatric patient and the first reported case in the intermediate junctional EB subtype. Case Presentation We report a case of a 3‐year‐old male with a known history of intermediate junctional EB, confirmed by whole exome sequencing to be a homozygous pathogenic frameshift mutation in COL17A1. He presented with polyuria and was later diagnosed with type 1 DM. Conclusion This report highlights the importance of recognizing systemic comorbidities in patients with rare structural genetic diseases like junctional EB.