Background: Malaria has long been known to human populations from across the world. Malaria remains the most important parasitic disease worldwide. Malaria is a potential medical emergency and should be treated accordingly. Routinely malaria is diagnosed using a combination of clinical observations, case history, and diagnostic tests, principally microscopic examination of stained slides. The objective of this study is to detect the flagging of malaria parasite in sysmex with correlation in peripheral smear and kit so that early detection of Malaria can be done with the most accurate result in lesser duration and cost. Among 99 positive cases, 85 were positive for P. vivax, 9 were positive for P. falciparum and 6 were positive for mixed infection. As compared to RDT, Sysmex flagging had 90.4% sensitivity; 56.3% specificity; 92.4% positive predictive value; 50.0% negative predictive value and 84.5% accuracy for detection of malarial parasite. Whereas when compared to PBS, Sysmex flagging had 90.9% sensitivity; 81.8% specificity; 97.8% positive predictive value; 50.0% negative predictive value and 90% accuracy for detection of malarial parasite. Sysmex flagging had moderate and significant agreement with both RDT and PBS assessments. Flagging had a detection rate of 66.7%, 94.1% and 80% respectively for P. falciparum, P. vivax and mixed infections. Conclusion: The findings of present study showed that Sysmex flagging is a cost-effective highly efficacious tool for screening of malaria parasite and it showed a high level of agreement with conventionally used laboratory tests as well as peripheral blood smear.