Background: Hematopoietic stem cell transplantation (HSCT) is the major curative therapy for myelofibrosis (MF) but carries a high risk of non-relapse mortality due to graft failure including graft-versus-host disease (GVHD). While prior literature suggests the potential benefits of Janus kinase (JAK) inhibition in treating acute or chronic GVHD, there is limited evidence on using JAK inhibitors (JAKi) as prophylaxis for post-transplantation outcomes in MF patients. This systematic literature review and meta-analysis aimed to assess survival outcomes and toxicities in MF patients who received JAKi as the prophylaxis against GVHD either peri- or post-transplantation. Methods: A systematic literature search was conducted through mid-2021 to identify relevant studies using Embase, PUBMED, and Cochrane Central Register of Controlled Trials (Database inception–July 6, 2021). Eligible study designs included randomized controlled trials and observational studies in adult patients with MF previously treated with JAKi for the prophylaxis against GVHD. The outcomes of interest were one- or two-year progression-free survival (PFS) rate, overall survival (OS) rates, incidence rate of chronic GVHD (cGVHD), and 100-day incidence rate of acute GVHD (aGVHD). Each outcome was pooled within meta-analyses of random effect methods. Results: A total of 13 clinical trials and prospective cohort studies including 684 patients with MF were identified for quantitative synthesis. All studies used ruxolitinib as a Janus kinase inhibitor (JAKi) treatment for prophylaxis against graft-versus-host disease (GVHD). Pooled 1- and 2-year PFS rate were 58% (95% CI: 47–69%) and 49% (95% CI: 38–60%), respectively. Pooled 1- and 2-year OS rate were 70% (95% CI: 59–81%) and 68% (95% CI: 47–90%), respectively. Pooled incidence rate of grade 2-4 and grade 3-4 aGVHD within 100 days were 26% (95% CI: 4%–48%), and 21% (95% CI: 5%–37%), respectively. Pooled incidence rate of 1- and 2-year cGVHD were 28% (95% CI: 17%-34%) and 44% (95% CI: 27%-61%), respectively. Conclusions: Ruxolitinibhas been introduced as the prophylaxis for GVHD in patients with MF receiving HSCT. Larger studies are warranted to investigate long-term outcomes, survival, and the optimal treatment duration.