This study aimed to explore the metabolic profiling in the serum of enterotoxigenic Escherichia coli (ETEC) infected piglets. Compared to control piglets, diarrheal piglets had higher contents of m-cresol and urocanic acid, but lower levels of fumaric acid, isoleucine, N-methyl-DL-alanine, 2-hydroxybutanoic acid, L-threose and putrescine, which are mainly associated with amino acid metabolism, energy metabolism and urea cycle. Compared to diarrheal piglets, recovered piglets had higher contents of oxoproline, proline, and ornithine, but lower contents of methyl phosphate, glycolic acid, myristic acid and azelaic acid, which are commonly involved in amino acid metabolism, glutathione synthesis and urea cycle. Collectively, the current study provides insights into metabolic alterations during ETEC infection and the recovery from ETEC induced diarrhea.