This paper aims to explore the gender gap in the academic performance in the secondary school in the Colombian regions using data from the SABER-11 2009, a test administered by the ICFES. This data has been analyzed using mean differences and through the student’s quantile regressions, focusing on the math and language components. This analysis shows that men obtain a better performance on the math component than women but this result is not homogenous in the country. Central-Eastern part of the country exhibit the wider differences. Solely in the Caribbean and Pacific region there were women having better performance in language.