Pancreatitis has been occasionally associated with Crohn's disease (CD). A definite etiology of pancreatitis can be identified in most patients, but a very small proportion remain idiopathic. We report a case of idiopathic pancreatitis resolved along with the clinical improvement of CD in a 25-year-old man. He presented with abdominal pain and diarrhea for 8 years. Ileocolonoscopy and enteroclysis showed multiple, longitudinal ulcers and strictures at the ileojejunum. The laboratory findings showed elevated serum amylase (951 IU/L) and lipase (326 IU/L) without positive autoantibodies. Esophagogastroduodenoscopy, enhanced pancreatic CT, and MRCP showed no abnormalities at ampulla of Vater, pancrease, and pancreaticobiliary duct. With the treatment with antibiotics, 5-aminosalicylic acid, steroid, and azathioprine, as a whole, decreasing pattern and intermittent fine coordinated fluctuation of the levels of amylase and lipase along with the decrease of Crohn's disease activity index (CDAI) and the CRP levels were observed. Then, three months after the start of the treatment, normalization of the pancreatic enzymes was observed, and there was recurrent elevation of pancreatic engyme during 12 months maintenance therapy. This report supports the concept of an association between idiopathic pancreatitis and CD, based on a significant and close relation between the levels of serum amylase and lipase, and CDAI.