Background Malaria and curable sexually transmitted infections (STI) are the most common curable infections known to have a severe impact on pregnancy outcomes in sub-Saharan Africa. This study aims to assess the marginal and joint prevalence of symptomatic cases of malaria and STI in pregnant women living in rural settings of Burkina Faso and their associated factors, after more than a decade of the introduction of intermittent preventive treatment (IPT-SP). Methods We carried out an observational study in two health districts in rural Burkina, namely Nanoro and Yako. Routine data were collected during antenatal and delivery visits for all women who delivered in the year 2016 and 2017. Logistic regression models were used to assess factors associated with infections. Results We collected data from 31639 pregnant women attending health facilities. Malaria, curable STI and their coinfections were diagnosed in 7747 (24.5%; 95%CI: 24.0–25.0%), 1269 (4.0%; 95%CI: 3.8–4.2%) and 388 (1.2%; 95%CI: 1.1–1.4%) women, respectively. In multivariate logistic regression, malaria occurrence was significantly higher in pregnant women < 20 years (Adjusted OR = 2.36; 95% CI: 2.07–2.69) than in women ≥30 years. The prevalence of curable STI was also significantly higher in students (Adjusted OR = 1.93; 95% CI: 1.26–2.95) and compensated workers (Adjusted OR = 1.52; 95% CI: 1.01–2.17) than in uncompensated workers. Women who received no IPT-SP had higher prevalence of malaria (Adjusted OR = 3.33; 95%CI: 3.00–3.70), curable STI (Adjusted OR = 1.96 95%CI: 1.60–2.39) and coinfections (Adjusted OR = 2.11; 95% CI: 1.50–2.95) compared to women who received SP. Conclusion Malaria and curable STI remain highly prevalent in rural settings of Burkina Faso, with young pregnant women and women who received no IPT-SP being the most affected. Prevention must be reinforced to improve maternal and infant health.