Mycosis fungoides is a primary cutaneous T-cell lymphoma with unfavorable prognosis for the advanced stages of the disease. Refractory disease and advanced-stage disease require systemic therapy. We report on a rare case of an atypical predominantly CD8+ folliculotropic mycosis fungoides (MF), a subtype of MF with poorer prognosis, in a 59-year-old woman, initially diagnosed with MF restricted to the skin- of T3N0M0B0/stage IIB according to the current WHO/EORTC classification. First-line treatment with local percutaneous radiotherapy in combination with systemic interferon alfa-2a resulted in complete remission. However, 21 months later the disease progressed to T3N0M1B0/stage IVB with development of cerebral manifestation and thus very poor prognosis. Allogeneic stem cell transplantation (SCT) was not a therapeutic option due to the lack of a suitable donor. We initiated methotrexate and cytarabin chemotherapy, followed by high-dose chemotherapy with thiotepa and BCNU with autologous SCT. Despite rapid response and complete remission of the cerebral lesions, disease recurrence of the skin occurred soon after. Interestingly, re-administration of interferon alfa-2a as a maintenance treatment after the salvage autologous SCT resulted in a durable complete remission during the follow-up period of currently 13 months after autologous SCT.