Objective Acanthamoeba is a free-living and opportunistic amoeba that the potential of this parasite to convert to a cyst, making its treatment difficult. In this study, we investigated the effect of microwave radiation on Acanthamoeba cysts in vitro. Methods Acanthamoeba cysts were reproduced in the culture medium. We divided 16 test tubes containing cysts into two groups. The contents of 8 tubes were irradiated with continuous microwave in the time range of 0-120 s, and the next 8 tubes were irradiated with repetitive microwave in the range of 0-360 s. The mortality of cysts at the end of irradiation was recorded and compared with control. Results Continuous and repetitive irradiation of microwave resulted in mortality of 100 (%) of Acanthamoeba cysts during 120 and 360 seconds, respectively. In continuous mode, parasite mortality in all groups was significantly different from the control group (P<0.0001). But in the repetition pattern only in groups that had been irradiated for more than 60 seconds, parasite mortality was significantly different from the control group (P<0.0001). Conclusion The change of radiation mode from continuous to repetitive, reduces the thermal effects of the microwaves but does not affect the mortality rate of Acanthamoeba cysts. Therefore, probably the impact of microwaves was not only caused by the increase in ambient heat but also its another property is involved in the death of Acanthamoeba.