CHD has been historically associated with the development of cerebral abscess. This retrospective cohort study examines the association of CHD with the occurrence of cerebral abscess in an inpatient paediatric population. We analysed data from the Pediatric Health Information System database, an administrative database that captures data from participating children’s hospitals in the United States. We included all patients admitted to participating paediatric ICUs between 2016 and 2021 for a total of 426,029 admissions. Including all admissions, 1,387 (0.3%) patients experienced a cerebral abscess, and of 80,927 (19%) patients with CHD, only 88 (0.1%) experienced a cerebral abscess (odds ratio 0.29, 0.23–0.36). Patients with seizures, cerebral oedema, stroke, shock, surgical intervention, and older age were associated with increased risk of development of a cerebral abscess. Interestingly, the development of a cerebral abscess was not associated with an increased risk of mortality (p = 0.937). When compared to patients without CHD admitted to the paediatric ICU, those with CHD appear less likely to develop a cerebral abscess. This study reiterates that cerebral abscess is a rare occurrence and does not demonstrate any significant association with CHD in a contemporary, inpatient population in the United States.