OBJECTIVE Balancing blood supply safety and sufficiency is challenging in malaria-endemic countries where the risk of transfusion-transmitted malaria (TTM) is ever-present. In support of reducing this risk, our study aimed at evaluating the performance of the Sysmex XN-31 analyser in blood donor malaria screening, as compared with current practice in Malawi. METHODS This prospective observational study was conducted on remnant venous donor blood samples collected at Malawi Blood Transfusion Service donation sites countrywide for routine blood-borne pathogen screening. XN-31 results were compared with routine thick smear malaria microscopy, using expert microscopy (phase 1 and 2) plus qualitative malaria polymerase chain reaction (PCR) (phase 2) to adjudicate discrepancies. RESULTS XN-31 detected malaria in 614 (11.6%) of 5281 study samples compared with 341 (6.5%) for routine microscopy. Of the 273 discrepant samples, 60 smears (phase 1) could not be retrieved for expert microscopic review. Expert microscopy confirmed the XN-31 positivity in 78.8% (149/189) and 91.7% (22/24) of discrepant samples in phase 1 (n = 4416) and phase 2 (n = 975), respectively, with two cases requiring PCR testing, confirming one each as positive and negative, giving sensitivities of 100% and 75% and specificities of 99.9% and 100%, respectively, for XN-31 and routine microscopy. CONCLUSIONS The automated Sysmex XN-31 analyser's high sensitivity and specificity, ability to detect all Plasmodium species and high throughput with rapid turnaround-time, overcomes many of the limitations of currently available diagnostic tests, making it well-suited for malaria screening of donated blood in malaria-endemic countries in support of TTM risk reduction.