Ruxolitinib (Rux), the first FDA-approved JAK inhibitor for the treatment of myelofibrosis (MF), was initially studied in patients who were ineligible for hematopoietic cell transplantation (HCT). However, the resultant decrease in splenomegaly and improvement in symptoms allowed some of the study patients to become HCT-eligible. We aimed to determine whether giving Rux to HCT-eligible MF patients would yield favorable HCT outcomes in relation to a historical cohort at our center. We conducted this single-arm Phase II prospective single-center study of Rux followed by HCT in adult patients with primary and secondary MF between 2014 and 2020. Patients were not required to have symptoms or splenomegaly. Patients took Rux for at least 8 weeks (no maximum) prior to the start of conditioning and tapered off by day -4 of HCT conditioning. A total of 101 patients were enrolled in the study (median age, 57 years; range, 34 to 71 years), of whom 61 (60%) proceeded to HCT (59% primary MF, 70% DIPSS [dynamic international prognostic scoring system] intermediate-2 or high-risk) after a median of 7 months (range, 2 to 89 months) on Rux. Patients engrafted at a median of 20 days; there was 1 primary graft failure. Nonrelapse mortality (NRM) was 13% at 1 year, compared to 26% in our historical cohort. With a median follow-up of 5.6 years among survivors, overall survival was 79% (95% confidence interval [CI], 69% to 90%) at 2 years, compared to 67% in our historical cohort, and 5-year survival was 74% (95% CI, 64% to 86%). The hazard ratio of death for those who had a Rux response relative to those who did not was 0.57 (95% CI, 0.20 to 1.61; P = .29). In this prospective Phase II study, patients receiving pre-HCT Rux had encouraging NRM and survival rates relative to historical patients at our center who proceeded to HCT without prior Rux.