Medication use is an important part of the health process and prevalence of its use among infants can reach up to 65% in their first months of life. The excessive use of medication could lead to an increase in their potential harm, surpassing their benefits. Considering this, this study aimed to describe medication use in children aged 3, 12, 24, and 48 months. Standardized questionnaires were applied to assess patterns and covariables of medication use. Medication use was investigated as an outcome and defined as the receipt of any medication within 15 days before the interview. Prevalence of medication use and 95% confidence intervals (95%CI) were described using chi-squared tests. Prescription source and frequency of use were also reported, along with the most frequent medication in each follow-up. Medication use prevalence was 67.2% (95%CI: 65.8; 68.6), 68.2% (95%CI: 66.8; 69.6), 52.4% (95%CI: 50.9; 54.0), 47.2% (95%CI: 45.7; 48.8), at 3, 12, 24, and 48 months, respectively. We observed a decrease in the proportion of medically prescribed medications and an increase in self-medication over the years. Drugs for gastrointestinal disorders (A03), vitamins (A11), analgesics (N02), anti-inflammatories (M01), and nasal formulations (R01) were the most frequently used medications. We found that children under four years of age comprised over 50% of the total use of medications and self-medication. These results highlight the need to warn caregivers on the importance of proper professional examination and prescription before they administer medications to children.