Like most malaria-endemic countries, Mozambique relies on tabulation of confirmed malaria test–positive febrile patients to track incidence of malaria. However, this approach is potentially biased by incidental malaria parasitemia in patients with fever of another etiology. We compared pan-Plasmodium aldolase and lactate dehydrogenase and Plasmodium falciparum histidine-rich protein 2 (PfHRP2) antigen concentrations measured using a laboratory bead-based assay of samples collected from 1,712 febrile and afebrile patients of all ages in Maputo, Zambézia, and Cabo Delgado provinces. We used a Bayesian latent class model to estimate the proportion of malaria-attributable fevers in malaria test–positive febrile patients. Depending on the antigen, estimated rates of malaria-attributable fever in malaria test–positive febrile patients were 100% in Maputo, 33–58% in Zambézia, and 63–74% in Cabo Delgado. Our findings indicate that most malaria test–positive febrile patients in the three provinces of Mozambique had a fever that was likely caused by the concurrent malaria infection. Counting malaria test–positive febrile patients for estimation of malaria incidence appears to be appropriate in this setting.