During the COVID-19 pandemic, patients in need of neurosurgical care suffered. Elective procedures were postponed, and emergency care visits decreased. Healthcare-associated ventriculitis (HAV) is a serious problem in children, with poor outcomes and frequent relapses. Our objective was to describe the clinical characteristics and the factors associated with a first HAV in children during two years of the pandemic. A retrospective cross-sectional study was performed from January 2021 to December 2022. The inclusion criteria were patients who developed a first HAV after a primary cerebrospinal fluid diversion procedure. The controls included patients without a first infection. Intraoperative and clinical data were extracted from medical records. A total of 199 CSF diversion surgeries were registered. A first infection occurred in 17 patients (8.5%), including 10 with external ventricular drain (EVD) and 6 with ventricular shunts. Gram-positive cocci were identified in 70.6%. Six patients recovered uneventfully, eight had relapse or superinfections, and three eventually died. Twenty patients were included as controls. Factors associated with a first infection were a younger age (median 9 vs. 102 months, p < 0.01), malnutrition (23.5% vs. 0%, p = 0.03), and an EVD placement (58.8% vs. 10%, p = 0.03). None of the intraoperative factors showed statistically significant differences. The rate of HAV was high. Most cases presented in children <1 year and with an EVD.