Objective: To follow up the refractory juvenile dermatomyositis (JDM) with autologous hematopoietic stem cell transplantation (AHSCT) in a long time and to investigate whether AHSCT is effective and safe to treat refractory JDM. Methods: We collected the AHSCT and follow-up data of three patients with refractory JDM who received autologous peripheral blood CD34+ cell transplantation in our hospital between June 2004 and July 2015. Those data include: hight, weight, routine blood and urine tests, ESR, CK, ALT, AST, LDH, renal functional tests, lymphocyte subpopulations, HRCT and muscle MRI. The last follow-up was done in June 2017. Results: All three patients had complete remission and could stop prednisone after 3-12 months. None of them relapsed at 144, 113 and 23 months follow-up. Twelve months after their AHSCT, all of their monitoring indexes have returned to normal and they have stopped all medications. Until the date of this article, none of them relapsed or need medicine. Conclusion: Our study suggests that AHSCT is safe and effective in treating refractory JDM, and it can provides long term drug-free survival. However, more cases are needed for further confirmation. © 2018 The Author(s).