Malaria rapid diagnostic tests (RDTs) are nowadays widely used in malaria endemic countries as an alternative to microscopy for the diagnosis of malaria. However, quality control of test performance and execution in the field are important in order to ensure proper use and adequate diagnosis of malaria. The current study compared the performance of a histidine-rich protein 2-based RDT used at peripheral health facilities level in real life conditions with that performed at central reference laboratory level with strict adherence to manufacturer instructions. Febrile children attending rural health clinics were tested for malaria with a RDT provided by the Ministry of Health of Burkina Faso as recommended by the National Malaria Control Programme. In addition, a blood sample was collected in an EDTA tube from all study cases for retesting with the same brand of RDT following the manufacturer's instructions with expert malaria microscopy as gold standard at the central reference laboratory. Fisher exact test was used to compare the proportions by estimating the p-value (p ≤ 0.05) as statistically significant. In total, 407 febrile children were included in the study and malaria was diagnosed in 59.9% (244/407) of the cases with expert malaria microscopy. The sensitivity of malaria RDT testing performed at health facilities was 97.5% and comparable to that achieved at the laboratory (98.8%). The number of malaria false negatives was not statistically significant between the two groups (p = 0.5209). However, the malaria RDT testing performed at health facilities had a specificity issue (52.8%) and was much lower compared to RDT testing performed at laboratory (74.2%). The number of malaria false positives was statistically significantly different between the two groups (p = 0.0005). Malaria RDT testing performed at the participating rural health facilities resulted in more malaria false positives compared to those performed at central laboratory. Several factors, including storage and transportation conditions but also training of health workers, are most likely to influence test performance. Therefore, it is very important to have appropriate quality control and training programmes in place to ensure correct performance of RDT testing.