This study generated quantitative proteomic data to investigate protein expression changes in the jejunum of yak calves following enterotoxigenic Escherichia coli (ETEC) challenge and Pediococcus pentosaceus NQ0729 supplementation. Yak calves were divided into three groups: a control group (CON), an ETEC-challenged group (ETEC), and a P. pentosaceus NQ0729-pretreated group followed by ETEC challenge (PET). Jejunal tissue samples were collected at the end of the animal trial and analyzed using LC-MS/MS-based quantitative proteomics. The dataset was used to compare protein abundance profiles among the three groups and to identify differentially expressed proteins and enriched biological pathways associated with ETEC challenge and probiotic intervention in yak calves.