Objectives: Congenital Zika Syndrome (CZS) has been linked to a wide spectrum of abnormalities. However, differences in hospitalization patterns between children with and without CZS have not yet been investigated. Methods: We compared rates of hospital admissions for all and specific diseases, proportions of admission causes, and total length of hospital stay (LOS) between children with CZS and those without the syndrome. Adjusted incidence rate ratios (aIRR) and aLOS were estimated using negative binomial regression. Results: Compared to those without CZS, the aIRR for all-cause hospitalizations in the CZS group ranged from 3.77 (95%CI: 3.47-4.06) in the neonatal period to 7.76 (95%CI: 6.91-8.61) at ages 2-4 years. Similar trends were observed for specific causes of admissions. Most admissions in the CZS group related to congenital malformations, neurological, respiratory and infectious diseases. aLOS ranged from 16.0 days [95%CI: 13.2-19.5] to 19.9 days among CZS patients and 6.0 days [95%CI: 5.9-6.2] to 9.3 days [95%CI: 9.3-9.4] for patients without the syndrome. Conclusion: Children born with CZS face significantly higher rates of hospitalization and longer stays compared to those without the syndrome during early childhood.