Objective To evaluate maternal and perinatal outcomes in cases of third‐trimester malaria (TTM). Methods A parity‐matched comparative cohort study was carried out between December 1, 2018, and April 30, 2019, in three university teaching hospitals in Yaoundé (Cameroon). Women with and without TTM were followed up till delivery. The variables analyzed included maternal and gestational ages at delivery, the regimen of intermittent preventive treatment, usage of insecticide‐treated net, history of malaria recorded during pregnancy, birth and placenta weights, Apgar score, and early neonatal outcomes. Fisher exact test, t‐test, and logistic regression were used for comparison. P<0.05 was considered statistically significant. Results Of 3063 pregnant women, 130 (4.2%) had TTM. Adverse outcomes associated with TTM were maternal anemia (relative risk [RR] 10, 95% confidence interval [CI] 4.91–20.34), intrauterine fetal demise (RR 7.50, 95% CI 1.47–38.06), preterm delivery (RR 4.50, 95% CI 2.37–8.51), low birth weight (adjusted RR 2.88, 95% CI 1.34–6.19), neonatal asphyxia especially if delivery occurred during parenteral treatment (RR 5.18, 95% CI 2.56–10.48), transfer of the newborn to the neonatal intensive care unit (RR 4.38, 95% CI 2.59–7.42), and intrapartum or early neonatal death (RR 4.18, 95% CI 1.48–11.74). Conclusion TTM was associated with adverse perinatal outcome especially if labor started during parenteral treatment.