ABSTRACT Introduction: Aerobic fitness is a component of physical fitness related to health and has great importance in the prevention of cardiovascular diseases. Objective: To verify the secular changes in aerobic fitness levels and to identify factors over a decade related to low levels of aerobic fitness in Brazilian children. Methods: This secular change study was carried out from 1999 to 2010 with 11,083 children aged from six to nine years, of both sexes, living in all regions of Brazil. The aerobic fitness was assessed by the 9-minute run test. The independent variables were sex, age, geographic region, area of residence, and nutritional status. The “t” test was used for independent samples and analysis of variance, chi-square test, and Poisson regression were used to estimate prevalence ratio (PR) and confidence intervals of 95% (CI 95%). Results: No significant changes in the distance covered in the 9-minute run test and in the prevalence of low levels of aerobic fitness were observed from 1999 to 2010. The population subgroups most likely to have low aerobic fitness levels were students aged seven years, those in the Midwestern, Southeast, and South of Brazil, those living in rural areas and those with overweight and obesity. Conclusions: Over a decade, low levels of aerobic fitness were present in four fifths of Brazilian children and this picture did not change. Low levels of aerobic fitness affected more children above six years old, living in the economically most favored regions of Brazil, in rural areas and with overweight.