Background Studies have examined the impact of contextual factors on the use of contraceptives among adolescents and found that many measures of income and social inequality are associated with contraceptive use. However, few have focused on maternal and primary health indicators and its influence on adolescent contraceptive use. This paper assesses whether maternal mortality rates, antenatal care visits, and primary healthcare coverage are associated with pill and condom use among female adolescents in Brazil. Methods We used data from the Study of Cardiovascular Risks in Adolescents (ERICA), a national, school-based cross-sectional study conducted in Brazil. A subsample of all female adolescents who had ever had sexual intercourse and were living in one of the 26 State capitals and the Federal District was selected (n = 7415). Multilevel mixed effects logistic regression models were estimated to examine the effect of contextual variables on pill and condom use. Results Sixty-five percent of female adolescents reported using pill while 21.9% reported using condom during the last sexual intercourse. Adolescents living in municipalities with low maternal mortality and high antenatal care coverage were significantly more likely to use pill during the last sexual intercourse compared to those from municipalities with high maternal mortality and low antenatal care coverage. Primary healthcare coverage (proportion of the population covered by primary healthcare teams) was not significantly associated with either condom or pill use during the last sexual intercourse. Conclusion Our findings suggest that promoting the use of pill among female adolescents may require approaches to strengthen healthcare systems rather than those focused solely on individual attributes.