To use the International Classification of Functioning, Disability and Health (ICF) to investigate whether children with congenital Zika Syndrome (CZS) show changes in their functioning and disability profile after nine months. This study included children with CZS recruited from a support centre for children with microcephaly in Brazil. The children's functional abilities and limitations were classified using ICF Core Set for children with cerebral palsy. Each ICF category was quantified in two moments with a mean interval of nine months. The study included 81 children (mean age = 38.4 ± 3.3mo). Most children showed changes between assessments. Categories that presented improvements were in body functions (five categories), environmental factors (two categories), and activity and participation (one category) sections. Most children with CZS evaluated improved their functioning and disability profile over time, mainly in body functions. These changes can be related to the course of the disease or to the health programmes that children had access.