Background: This study describes medication use by women up to 3 months postpartum and evaluates the association between medication use by women who were still breastfeeding at 3 months postpartum and weaning at 6 and 12 months. Methods: Population-based cohort, including women who breastfed (n = 3988). Medications were classified according to Hale’s lactation risk categories and Brazilian Ministry of Health criteria. Duration of breastfeeding was analysed using Cox regression models and Kaplan-Meier curves, including only women who were still breastfeeding at three months postpartum. Results: Medication use with some risk for lactation was frequent (79.6% regarding Hale’s risk categories and 12.3% regarding Brazilian Ministry of Health criteria). We did not find statistically significant differences for weaning at 6 or 12 months between the group who did not use medication or used only compatible medications and the group who used medications with some risk for lactation, according to both criteria. Conclusions: Our study found no association between weaning rates across the different breastfeeding safety categories of medications in women who were still breastfeeding at three months postpartum. Therefore, women who took medications and stopped breastfeeding in the first three months postpartum because of adverse side-effects associated with medications could not be addressed in this analysis.