We report a case of an adolescent girl with atypical manifestations of pancreatitis with autoimmune phenomenon presenting with epigastralgia and back pain. While no abnormalities were detected on computed tomography and magnetic resonance imaging, apart from the absence of peripancreatic spread, laboratory and serological findings, such as hypergammaglobulinemia, a high titer of immunoglobulin G, a high titer of immunoglobulin G4, slight positivity for antinuclear antibodies, and positivity for autoantibodies to lactoferrin, were suggestive of autoimmune pancreatitis (AIP). Magnetic resonance cholangiopancreatography imaging (MRCP) visualized only the main pancreatic duct (MPD) in the pancreas head region. Proteoclastic enzyme inhibitor treatment was ineffective but the patient responded well to oral prednisolone. The patient and her family did not consent to endoscopic retrograde pancreatography or biopsy/histopathological examination. The case could not be diagnosed as AIP due to lack of typical diagnostic criteria, and thus the final diagnosis was considered pancreatitis with autoimmune phenomenon. We considered that the MRCP finding of partly visible MPD was due to diffuse irregular narrowing of the MPD. This case suggests that while MRCP imaging of the MPD may be helpful in the diagnosis of pancreatitis with autoimmune phenomenon, a negative result does not preclude such diagnosis.