Naegleria fowleri is a free-living amoeba commonly found in the environment, mainly in fresh water and soil. This protozoon is occasionally involved in cases of fatal central nervous system disease in humans and other animal species. We describe here a case of meningoencephalitis due to Naegleria fowleri in cattle, in southern Brazil. A four-year-old Angus cow presented a clinical history of initial mild neurological signs that progressed to paddling movements, opisthotonus and lateral recumbency after five days. This animal had been kept in an irrigated rice stubble paddock. Grossly, the main lesions consisted of multiple areas of malacia in the right olfactory bulb, piriform lobes, hippocampus, frontal lobe cortex and fornix, along with severe thickening of the mesencephalon and rhombencephalon leptomeninges. Microscopically, severe multifocal necrosuppurative and hemorrhagic meningoencephalitis associated with a large quantity of amoebic trophozoites was present. The latter were confirmed to be Naegleria spp., through immunohistochemistry. Based on the strong congruence with the histopathological data of known cases reported in the literature, a probable association with Naegleria fowleri was established. To our knowledge, this is only the second report of Naegleria fowleri-associated meningoencephalitis in cattle in South America, and it is the first in southern Brazil.