Achievement gaps refer to the difference in the performance on assessments of students belonging to different social groups. Achievement gaps between ethnic groups have been observed in countries with heterogeneous populations. In this paper, achievement gaps between ethnic populations in Brazil were analyzed by studying the performance of a large cohort of senior high-school students in a standardized national exam. Ethnic groups were stratified by Brazilian states and socio-economic variables to homogeneize the groups, and the analyses focused on the disciplines of mathematics and writing that involve different cognitive functions. AWelch’s t-test analysis was performed and key socio-economic variables that may explain the gaps were studied. The results show that gaps between ethnic groups of students living in low-income households were either statistically insignificant or small (2–6%) if statistically significant. Larger gaps however were observed for students coming from high-income families in some contexts. Although parental education was associated with higher performance, it may either increase, decrease or maintain the gaps between White and Black, and between White and Pardo students. Our results support that socio-economic variables, linked to historical developments, have an impact on student’s performance irrespective of ethnic background, resulting on little to no influence on group performance when students are exposed to similar cultural and economic contexts.