Neurological complications remain an important source of morbidity after heart transplantation, but their contemporary incidence, determinants, and clinical consequences are not fully characterized. This study evaluated the incidence, risk factors, in-hospital outcomes, and long-term survival associated with neurological complications after heart transplantation in a single-center cohort. A single-center retrospective cohort study was performed on 641 heart transplant recipients. Patients were divided according to the occurrence of post-transplant neurological complications. Neurological events were further categorized as transient or permanent neurological dysfunction. Preoperative, intraoperative, and postoperative variables were compared. To reduce overfitting, the multivariate logistic regression model was restricted to six clinically relevant variables associated with neurological complications at univariable analysis. Overall survival was evaluated using Kaplan–Meier analysis and compared with the log-rank test. Univariable Cox proportional hazards regression was performed to assess the association between neurological complications and long-term mortality. Neurological complications occurred in 65 of 641 recipients (10.1%). Transient neurological dysfunction was observed in 55 patients (8.6%), whereas permanent neurological impairment occurred in 24 recipients (3.7%). Some patients experienced both transient and persistent neurological manifestations; therefore, these categories were not mutually exclusive. Preoperative extracorporeal membrane oxygenation (ECMO) support (18.5% vs. 8.2%, p = 0.006), mechanical ventilation (16.9% vs. 8.7%, p = 0.03), previous cardiac surgery (44.6% vs. 26.6%, p = 0.002), and pretransplant acute kidney injury (21.5% vs. 8.5%, p = 0.001) were associated with a higher incidence of neurological complications. Recipients developing neurological events also exhibited higher rates of cytomegalovirus (CMV)-seropositive donors (36.2% vs. 16.6%, p = 0.001) and postoperative CMV infection (23.8% vs. 13.2%, p = 0.03). Neurological complications were associated with prolonged intensive care unit stay, increased postoperative organ dysfunction, greater transfusion requirements, and higher in-hospital mortality. At multivariate analysis, previous cardiac surgery (OR 1.81, 95% CI 1.00–3.24; p = 0.047), pretransplant acute kidney injury (OR 2.15, 95% CI 0.98–4.46; p = 0.047), donor traumatic brain injury (OR 2.34, 95% CI 1.16–4.53; p = 0.014), and donor CMV seropositivity (OR 2.52, 95% CI 1.36–4.56; p = 0.003) emerged as independent predictors of neurological complications. At a median follow-up period of 7 years (IQR, 1.2–12.7 years), recipients with neurological complications experienced significantly lower overall survival than those without neurological complications (log-rank p < 0.001). Neurological complications were associated with a two-fold higher risk of long-term mortality (HR 2.06, 95% CI 1.33–3.18; p = 0.001). Neurological complications after heart transplantation remain a major source of postoperative morbidity and are associated with increased mortality, multiorgan dysfunction, and significantly reduced long-term survival. Previous cardiac surgery, pretransplant acute kidney injury, and CMV-seropositive donor status independently predicted neurological complications, supporting the contribution of surgical complexity, systemic vulnerability, and immunological factors to neurological risk.