A 76-year-old Japanese man was admitted to our hospital because of the occurrence of multiple nodules on the shaft of his penis. He was diagnosed with diffuse large B cell lymphoma (DLBCL). His lymphoma was located only in his penis. He received immunochemotherapy and involved-field radiotherapy, and achieved complete response (CR). About two years later, he complained of a poor appetite. Magnetic resonance imaging showed a mass lesion in the pituitary stalk. Biopsy of this mass revealed the recurrence of DLBCL. He received whole-brain radiotherapy, and achieved CR. This is the first case of an isolated pituitary stalk relapse of primary penile lymphoma.