Despite aggressive treatment, canine parvovirus (CPV) enteritis remains a major cause of morbidity and mortality in puppies. Identifying reliable biomarkers of CPV enteritis is important for determining severity, length of hospital stay, and predicting clinical outcomes. This the first study that aims to emphasize the relevance of the manuscript. Forty-three (43) CPV-infected dogs were diagnosed by a rapid antigen test kit and subsequent PCR, and 10 healthy dogs were enrolled. In this prospective study, metabolomics and cardiac troponin were measured by NMR and ELISA, respectively. The diseased dogs showed statistically significant lower levels of fructose, glucose, citrate, glycerate, glutamate, carnitine, glycine, formate, and higher levels of isoleucine, isovalerate, glycolate, and creatine compared with healthy dogs. The same analysis performed on lipid parameters showed statistically significant higher levels of cholesterol variants, fatty acyl variants, free cholesterol, glycerol backbone, and sphingomyelin and lower levels of phosphoglycerates and esterified cholesterol in the diseased groups. The changes in metabolomics could be attributed to energy deficit, fat mobilization, gluconeogenesis, tricarboxylic acid cycle deficiency, and multiple organ failure. Decreased citrate, and increased fatty acyl chain-CH2CO and sphingomyelin levels will serve as the most useful biomarkers in the prognosis of dogs suffering from CPV infection.