Myelofibrosis (MF) is a chronic myeloproliferative neoplasm characterized by bone marrow fibrosis, ineffective hematopoiesis, splenomegaly, constitutional symptoms, and shortened survival. Patients often experience multiple disease-associated, as well as treatment-emergent, cytopenias, including thrombocytopenia. However, patients with MF with thrombocytopenia have few therapeutic options, and there is little information on the management of these patients. Several Janus kinase (JAK) inhibitors have been developed for the treatment of MF, with one (ruxolitinib) having been approved. However, given their mechanism of action, JAK inhibitors are associated with high rates of thrombocytopenia. Patients can be successfully managed with dose modifications, but little is known about the safety and efficacy of these agents in patients with thrombocytopenia. Recent studies of JAK inhibitors in patients with MF who have low platelet counts have had mixed results. This review discusses the prevalence, prognostic implications, and management of thrombocytopenia in MF and the different therapeutic options available for this patient population, with an emphasis on current clinical experience with targeted therapies, as well as recent findings from several clinical studies currently underway.