We describe a rare case of discordant lymphoma characterized by the coexistence of diffuse large B-cell lymphoma (DLBCL) in the brain and mantle cell lymphoma (MCL) in the colon, rectum, and bone marrow. A 63-year-old male patient with consciousness impairment and gait disturbance was admitted to our institution. Head computed tomography scan and contrast-enhanced magnetic resonance imaging showed a mass in the right temporal lobe and rectal wall thickening. Brain biopsy revealed DLBCL, and bone marrow and rectum biopsy showed MCL. According to a polymerase chain reaction analysis of immunoglobulin heavy-chain gene rearrangements using brain and bone marrow specimens, the two lesions were clonally unrelated lymphomas. After five cycles of R-MPV (rituximab, methotrexate, procarbazine, vincristine) therapy and three cycles of R-ESHAP (rituximab, etoposide, cytarabine, cisplatin, methylprednisolone) therapy, the patient received autologous hematopoietic stem cell transplantation using R-MEAM (rituximab, ranimustine, etoposide, cytarabine, melphalan) regimen after bridging therapy with ibrutinib. In addition, he received whole-brain irradiation at a dose of 40 Gy in 20 fractions as consolidation therapy. He did not relapse within 3 years of transplantation. To the best of our knowledge, this is the first case report of DLBCL and MCL coexistence.