Background: Neurological complications (NCs) are of major concern following hematological stem cell transplantation (HSCT), most of which present with seizures. Procedures: We performed a retrospective study (2002–2018) of patients undergoing HSCT in order to analyze the incidence and aetiologies related to seizures. Results: Of 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). Conclusions: Neurological complications highly impact survival and outcomes and need to be addressed when facing an HSCT procedure. [ABSTRACT FROM AUTHOR]