Malaria remains a significant global health burden, with ∼263 million cases across 83 countries. It is essential to quickly and accurately detect cases to control the spread of the disease. Given the widespread use of malaria rapid diagnostic tests (mRDTs) for case management and surveillance, it is crucial to understand test reliability. Clarifying how mRDT results differ from real-time polymerase chain reaction (qPCR) test results, as well as the nature of additional variance by test manufacturer, will be useful for reducing measurement bias. After comparing three national standard mRDTs and a research mRDT with qPCR results from a 2021 cross-sectional study in Tanzania, differences were found in terms of age, sex, and regional malaria transmission rate. The research test underperformed overall, with poor sensitivity across transmission strata. After comparing the research mRDT to standard mRDTs, the odds ratios indicated that transmission intensity may affect mRDT agreement and diagnostic performance. These results offer pertinent information on test accuracy and decrease outcome misclassification for malaria prevalence.