Background Malaria infection affects the immune response to some vaccines. As Ebola virus (EBOV) outbreaks have occurred mainly in malaria-endemic countries, we have assessed whether asymptomatic malaria affects immune responses to the 2-dose Ad26.ZEBOV, MVA-BN-Filo Ebola vaccine regimen. Methods In this sub-study of the EBOVAC-Salone Ebola vaccine trial in Sierra Leone, malaria microscopy was performed at the time of Ebola vaccination. Participants with symptomatic malaria were treated before vaccination. Ebola vaccine responses were assessed post-dose 1 (day 57) and post-dose 2 (day 78) by the EBOV glycoprotein FANG enzyme-linked immunosorbent assay (ELISA), and responses expressed as geometric mean concentrations (GMCs). Geometric mean ratios (GMRs) of the GMCs in malaria-positive versus malaria-negative participants were derived with 95% confidence intervals (CIs). Results A total of 587 participants were studied, comprising 188 adults (≥18 years) and 399 children (in age groups of 12–17, 4–11, and 1–3 years). Asymptomatic malaria was observed in 47.5% of adults and 51.5% of children on day 1. Post-dose 1, GMCs were lower in 1–3-year-old malaria-positive compared with malaria-negative children (age group–specific GMR, .56; 95% CI, .39–.81) but not in older age groups. Post-dose 2, there was no consistent effect of malaria infection across the different age groups but there was a trend toward a lower response (GMR, .82; 95% CI, .67–1.02). Conclusions The Ad26.ZEBOV, MVA-BN-Filo Ebola vaccine regimen is immunogenic in participants with asymptomatic malaria. Therefore, it is not necessary to screen for asymptomatic malaria infection prior to vaccination with this regimen.