Abstract Encephalomyocarditis virus is responsible for epizootics and sporadic mortalities worldwide, particularly in zoos, and in non‐rodent species is characterised by sudden death due to acute myocarditis. Rodents are considered the reservoir host and show variable manifestations ranging from clinically asymptomatic infection to paralysis or death. We present a capybara ( Hydrochoerus hydrochaeris ) that exhibited lethargy, ataxia, nasal discharge and bradyarrhythmias over 5 days before death. Encephalomyocarditis virus infection was confirmed by histopathology, which showed non‐suppurative myocarditis with necrosis and polymerase chain reaction, and occurred despite recent vaccination.