BackgroundNeurological complications (NCs) are of major concern following hematological stem cell transplantation (HSCT), most of which present with seizures.ProceduresWe performed a retrospective study (2002–2018) of patients undergoing HSCT in order to analyze the incidence and aetiologies related to seizures.ResultsOf 155 children undergoing HSCT, 27 (17.4%) developed seizures at some point in 2 years of follow‐up. The most frequent etiologies were central nervous system (CNS) infection (n = 10), drug toxicity (n = 8), and vascular disease (n = 5). A statistically significant association was found between seizure and the HSCT type (lower risk for a related identical donor, p = .010), prophylactic or therapeutic mycophenolate use (p = .043 and .046, respectively), steroid use (p = .023), selective CD45RA+ depletion (p = .002), pre‐engraftment syndrome (p = .007), and chronic graft‐versus‐host disease (GVHD) severity (p = .030). Seizures predicted evolution to life‐threatening complications and admission to intensive care (p < .001) and higher mortality (p = .023). A statistically significant association was also found between seizures and sequelae in survivors (p = .029). Children who developed seizures had a higher risk of CNS infection and vascular disease (odds ratio 37.25 [95% CI: 7.45–186.05] and 12.95 [95% CI 2.24–74.80], respectively).ConclusionsNeurological complications highly impact survival and outcomes and need to be addressed when facing an HSCT procedure.