BackgroundLack of valid and reliable data on malaria deaths continues to be a problem that plagues the global health community. To address this gap, the verbal autopsy (VA) method was developed to ascertain cause of death at the population level. Despite the adoption and wide use of VA, there are many recognized limitations of VA tools and methods, especially for measuring malaria mortality. This study synthesizes the strengths and limitations of existing VA tools and methods for measuring malaria mortality (MM) in low- and middle-income countries through a systematic literature review.MethodsThe authors searched PubMed, Cochrane Library, Popline, WHOLIS, Google Scholar, and INDEPTH Network Health and Demographic Surveillance System sites’ websites from 1 January 1990 to 15 January 2016 for articles and reports on MM measurement through VA. Inclusion criteria: article presented results from a VA study where malaria was a cause of death; article discussed limitations/challenges related to measurement of MM through VA. Two authors independently searched the databases and websites and conducted a synthesis of articles using a standard matrix.ResultsThe authors identified 828 publications; 88 were included in the final review. Most publications were VA studies; others were systematic reviews discussing VA tools or methods; editorials or commentaries; and studies using VA data to develop MM estimates. The main limitation were low sensitivity and specificity of VA tools for measuring MM. Other limitations included lack of standardized VA tools and methods, lack of a ‘true’ gold standard to assess accuracy of VA malaria mortality.ConclusionsExisting VA tools and methods for measuring MM have limitations. Given the need for data to measure progress toward the World Health Organization’s Global Technical Strategy for Malaria 2016–2030 goals, the malaria community should define strategies for improving MM estimates, including exploring whether VA tools and methods could be further improved. Longer term strategies should focus on improving countries’ vital registration systems for more robust and timely cause of death data.Electronic supplementary materialThe online version of this article (doi:10.1186/s12936-017-2071-x) contains supplementary material, which is available to authorized users.