Naegleria fowleri, a pathogenic free-living amoeba, leads to a fatal infection known as primary amebic meningoencephalitis (PAM) in human and animals. PAM is an acute, fulminant, necrotizing, and hemorrhagic disease that leads to death in approximately seven days. In this study, we investigate the cytotoxicity of target cells and the secreted molecules of N. fowleri under the non-contact condition. The target cell (U87MG cell) treated with N. fowleri lysates showed no morphological changes and no cytotoxicity. By contrast, the U87MG cells co-cultured with N. fowleri trophozoites under the non-contact condition induced morphological changes and reduction in number. When U87MG cells were co-cultured with N. fowleri trophozoites under the non-contact condition for 30 min, 2 hr, and 4 hr, the levels of cytotoxicity of target cells were 32.3, 35.5, and 37.8%, respectively. Particularly, when the ratio of amoeba to target cells is 10 to 1, the level of cytotoxicity of target cells was 49.7% at 30 min. To show the proteins secreted from N. fowleri under the non-contact condition, we carried out 2D electrophoresis and observed 6 major proteins. Finally, these results suggest that the molecules released from N. fowleri under the non-contact condition induce the cell death and this process is an important step in pathogenesis of N. fowleri.