Objective: Malaria is one of the most important parasitic diseases and one of the important health issues especially in tropical and subtropical countries. The importance of this disease is due to its high prevalence and mortality, as well as drug resistance and side effects of common drugs used for its treatment. Snake venom is a complex mixture of active pharmaceutical ingredients. The present study aims to investigate the anti-Plasmodium falciparum activity of the purified fractions isolated from the venom of Iranian cobra snake (Naja Naja Oxiana) by real-time Polymerase Chain Reaction (PCR) method. The importance of this disease is due to its high prevalence, significant mortality, as well as drug resistance and, side effects of current drugs in treatment. Venom is a complex mixture of active pharmaceutical ingredients. The purpose of this study was to investigate the anti-Plasmodium falciparum activity of the purified fraction of Iranian cobra snake venom by Real -time PCR. Methods: After preparation and purification of lyophilized venom for determining the parasitic load, different fractions obtained from the venom of Naja Naja Oxiana put in different plates adjacent to Plasmodium falciparum (3D7) strain in the ring stage. The degree of parasitemia was determined by real-time PCR. Finally, the effective fraction with anti-malaria properties was identified. Results: The active fraction with a half maximal inhibitory concentration of 0.026 μg/mL was the most effective fraction on Plasmodium falciparum in vitro (P<0.001). Conclusion: The active fraction of Naja Naja Oxiana venom at the mentioned concentration has anti-malaria effect. This results can motivate the continuation of further research in this field.