Continuous monitoring of malaria epidemiology is needed in malaria-endemic settings to inform malaria control and elimination strategies. This study aimed to compare the malariometric indices between the under-fives and school-age children. We surveyed children aged 1.5 to 12 years for plasmodia carriage with the aim of including them in a longitudinal follow-up cohort. The survey took place from 7–11 September 2020 in a southwest area of Burkina Faso. Clinical and demographic data including malaria control measures were collected. A finger prick blood sample was taken for haemoglobin testing, and blood smears and dried blood spot preparation. The malariometric indices were calculated and compared between school-age children and those under the age of five. Multiple logistic regression was fitted to assess the association between malaria parasite carriage and age categories. Based on the PCR results, the parasite prevalence was 21.4% in the under-fives versus 44.2% in school-age children (p-value < 0.0001), with a pooled prevalence of 32.7% (CI = [28.8, 36.8]). The gametocyte prevalence was also significantly higher in school-age children (11.9%) compared to the under-fives (3.7%). Adjusted for covariates, school-age children were 2.9 times (IC = [2.0, 4.2]) more likely to carry the asexual parasite, compared to the under-fives. Malaria was moderate and stable endemic in this area and school-age children play a key role in the spread of the disease. The WHO conditional recommendation for intermittent preventive treatment of malaria in school-aged children living in malaria-endemic settings with moderate to high perennial or seasonal transmission should be implemented.