This paper investigates quality with equity in Brazilian schools, an important current challenge for the role of education in an unequal society. The comparison between results of the three cycles of basic education (5th, 9th and 12th grades) revealed a systematic decrease in equity throughout schooling. Multilevel modeling was conducted for the ninth year of 11,810 public schools in six Brazilian states, three of high per capita income (Rio Grande do Sul, Santa Catarina and São Paulo) and three of low per capita income (Alagoas, Ceará and Maranhão). The school indicators of effectiveness and equity showed a negative correlation (r = -0.58). We found 41% of schools with effectiveness above the median in both Saeb assessments and 6% also showed equity above the median in both tests. The results suggest that quality with equity is indeed a challenge. In order to achieve this objective, the following are especially important: salary appreciation of teachers and principals; principals experience; creative teaching; availability of teaching resources for the teacher; safe school environment with common areas. Regarding public policies, the results suggest the need for material and immaterial valuation of education professionals, especially in contexts of great inequality and recent expansion of the public education system.