Epsilon toxin (Etx) is an extremely potent toxin produced by Clostridium perfringens toxinotypes B and D, which cause fatal enterotoxemia in many livestock species, mainly sheep and goats. Our previous study demonstrated that the aromatic amino acid (AA) residue at position 71 in domain III of Etx is needed for its cytotoxic activity toward MDCK cells. Here, we first determined that Etx mutants with non-aromatic AA substitutions at Tyr71 lost lethality in mice, indicating that the aromatic AA residue at position 71 is a toxicity determinant of Etx in vivo. After intravenous injection with a high dose of the trypsin-activated Etx-Y71A mutant, mice did not show any histopathological lesions, and confocal microscopy observations further showed that Etx-Y71A lost the ability to cross the blood-brain barrier of the mice. These results suggested that the Etx-Y71A mutant is sufficiently safe in vivo to be a vaccine candidate. Furthermore, the immune efficacy of Etx-Y71A was evaluated in model and host animals. Mice inoculated with this mutant produced high levels of neutralizing antibodies and were completely protected from a 100 LD of trypsin-activated Etx challenge. Sheep immunized with Etx-Y71A produced high levels of neutralizing antibodies that provided protection in mice against an activated Etx challenge, and lambs could receive passive immunity through immunization of pregnant ewes. Additionally, homology modeling and circular dichroism analysis showed that Etx-Y71A has structural similarity to Etx, which provides a structural basis for Etx-Y71A retaining the immunogenicity of Etx. Taken together, these results suggest that Etx-Y71A is a potential vaccine candidate against Etx-inducing enterotoxemia.