The objective of this study is to describe the neurologic, neurocognitive, and functional outcomes of children aged under 6 years supported on the Berlin Heart EXCOR ventricular assist device (VAD) followed in the Complex Pediatric Therapies Follow-up Program (CPTFP). Sixteen patients were prospectively followed through this longitudinal, developmental program. The patients were evaluated with neurologic physical examination. Intelligence quotients (IQ) and functional outcome scores (ABAS-II scores) were obtained. Neuroimaging reports from before, during, and after VAD implantation were retrospectively reviewed for reported brain injury (BI). Twelve patients (75%) had neuroimaging documented BI at some point in their life (i.e., before, during, or after VAD support). Five patients (31%) had neuroimaging evidence of acute BI incurred while on the VAD. The high overall number of patients with neuroimaging documented BI at any point in their life illustrates that the risk for BI also exists outside the window of VAD support. Patients with abnormal neurologic physical examination at follow-up had lower IQ and ABAS-II scores compared with patients with normal neurologic physical examination (mean full-scale IQ 66.9 vs. 95.0, p = 0.001; mean ABAS-II 66.3 vs. 94.2, p < 0.001).