Enteric protozoan infections—cryptosporidiosis, giardiasis, microsporidiosis, and coccidiosis—constitute a significant global burden on human and animal health. Yet comprehensive parasitological surveys of wildlife in the eastern Tibetan Plateau, where anthropogenic, livestock, and wildlife activities extensively intersect, remain deficient. We collected 359 fecal specimens from wild carnivores across 98 random quadrats and employed molecular techniques for host identification and protozoan screening. Seven carnivore species were identified, with Tibetan fox (Vulpes ferrilata) predominating. Intestinal protozoa were exclusively recovered from Vulpes species, yielding a prevalence of 19.37% (68/351; 95% CI, 15.24%–23.51%). Eimeria falciformis (7.41%, 26/351) and Eimeria banffensis (7.12%, 25/351) were the most frequently detected, followed by Enterocytozoon bieneusi (3.70%, 13/351). Cryptosporidium was confirmed in one V. ferrilata, and Giardia intestinalis in 2 samples (V. ferrilata and Vulpes vulpes). This investigation furnishes the first molecular evidence that wild carnivores, especially V. ferrilata, harbor zoonotic protozoa including G. intestinalis assemblage AII and E. bieneusi genotypes PigEBITS5 and a D-like variant. The concurrent detection of Cryptosporidium yak genotype and E. bieneusi subgroup 1i in foxes, pikas, yaks, and sheep implies potential interspecies transmission at the wildlife–livestock interface. These findings fill knowledge gaps in regional parasite diversity and emphasize the need for enhanced surveillance of wildlife-borne protozoa under a One Health framework, thereby providing scientific evidence for zoonotic risk assessment and public health planning.