Background:: Autologous hematopoietic stem cell treatment (AHSCT) is considered an effective treatment option for patients with aggressive relapsing-remitting multiple sclerosis (RRMS). Still there are few randomized and controlled studies of AHSCT to shed light on the safety and efficacy of the treatment, and therefore experiences from single centers are important. Aim: To describe the Danish experience with AHSCT regarding patient characteristics, safety, and efficacy. Method: Nationwide retrospective single center study of patients with multiple sclerosis (MS) treated with AHSCT. Results: A total of 32 patients were treated with AHSCT from May 2011 to May 2021. Seven were treated with carmustine, etoposide, cytarabine arabinoside, and melphalan (BEAM) as well as antithymocyte globulin (ATG). Twenty-five patients were treated with cyclophosphamide (CY) and ATG. In the whole cohort, relapse-free survival (RFS) was 77% (95% CI: 64–94%), worsening-free survival (WFS) was 79% (95% CI: 66–96%), MRI event-free survival (MFS) was 93% (95% CI: 85–100%), and no evidence of disease (NEDA-3) was 69% (95% CI: 54–89%) at the end of year two post-AHSCT. We had no treatment related mortality and only few severe adverse events (AEs). Conclusion: AHSCT of patients with aggressive RRMS was an effective and relatively safe treatment with few serious AEs and no mortality in Danish patients.