Neurologic complications (NCs) may be a significant source of morbidity and mortality after hematopoietic cell transplantation (HCT). We performed a retrospective study of 263 consecutive patients undergoing allogeneic HCT for hematological malignancies to determine the incidence, risk factors and clinical impact of NCs in the first 5 years after HCT. We determined the incidence of central nervous system (CNS) infection, intracranial hemorrhage, ischemic stroke, metabolic encephalopathy, posterior reversal encephalopathy syndrome, seizure and peripheral neuropathy. In all, 50 patients experienced 63 NCs—37 early (≤ day + 100), 21 late (day +101 to 2 years) and 5 very late (2 to 5 years). The 1- and 5-year cumulative incidences of all NCs were 15.6% and 19.2%, respectively, and of CNS complication (CNSC; all of the above complications except peripheral neuropathy) were 12.2 and 14.5%. Risk factors for CNSC were age (hazard ratio (HR) = 1.06 per year, P = 0.0034), development of acute GvHD grade III-IV (HR = 2.78, P=0.041), transfusion-dependent thrombocytopenia (HR = 3.07, P = 0.025) and delayed platelet engraftment (> 90th centile; HR = 2.77, P = 0.043). CNSCs negatively impacted progression-free survival (HR = 2.29, P = 0.0001), overall survival (HR = 2.63, P < 0.0001) and nonrelapse mortality (HR = 8.51, P < 0.0001). NCs after HCT are associated with poor outcomes, and usually occur early after HCT.