Objective The objective of the study is to evaluate cross-sectional and longitudinal changes in children's commuting to school in a representative sample of a Brazilian city. Methods Two school-based studies were carried out in 2002 (n = 2936; 7–10 years old) and 2007 (n = 1232; 7–15 years old) in Florianopolis, Brazil. Cross-sectional data were collected from children aged 7 to 10 years in 2002 and 2007. Longitudinal analyses were performed with data from 733 children participating in both surveys. Children self-reported their mode of transportation to school using a validated illustrated questionnaire. Changes were tested with chi square statistics and McNemar's test. Results Cross-sectional data showed a 17% decline in active commuting; a decrease from 49% in 2002 to 41% in 2007. On the other hand, active commuting among the 733 children increased as they entered adolescence 5 years later, rising from 40% to 49%. Conclusion Active commuting to school decreased in Brazilian children aged 7–10 years over a five year period; whereas, it increased among children entering adolescence. Policies should focus on safety and environmental determinants to increase active commuting.