Women’s health assistance at the low-complexity level is focused on the most common diseases and can be affected by primary health care coverage, particularly in areas far away from large urban centers. Thus, in this work, we aim to analyze the relationship between socioeconomic status, health care indicators, and primary care coverage in mortality from neoplasms of the lower genital tract and breast in Brazilian women during reproductive and non-reproductive periods. We conducted an ecological study at the Gynecology Discipline, Medicine School, University of São Paulo. Secondary data were collected from women according to reproductive periods and mortality data from the Mortality Information System based on International Classification of Disease—10th edition regarding breast and lower genital tract neoplasms in 2017. The health service and socioeconomic indicators were obtained from the Informatics Department of the Unified Health System and Brazilian Institute of Geography and Statistics. Our results showed that primary care coverage and health service indicators were not associated with mortality from breast cancer and the female lower genital tract, both in reproductive and non-reproductive periods. Sociodemographic indicators were found to be associated with mortality from breast cancer and the female lower genital tract, with income being associated with reproductive period (β = −0.4; 95% CI, −0.8 to −0.03) and educational level in the non-reproductive period (β = 9.7; 95% CI, 1.5 to 18.0).