The probiotic Enterococcus faecium is a gut microbe with immunomodulatory effects, which has been widely used to prevent diarrhoea in pigs and birds. Escherichia coli is a common pathogen that causes inflammatory bowel disease in animals. The aim of this study was to investigate the protective effects of E. faecium on enteritis in goats. Forty goats were randomly divided into 4 treatment groups: control, E. faecium, E. coli, and E. faecium + E. coli. The changes of physiological indicators and diarrhoea scoring were evaluated on days -4, -2, 0, 2, 4, 6, and 8. The pathological examination, inflammatory cytokines mRNA expression and bacterial counts in jejunum and caecum were detected on day 4 and 8. The results showed that body temperature, respiratory rate, heart rate and leukocyte counts all increased from the 2nd to the 6th day after feeding with E. coli, and the diarrhoea score was significantly increased. However, E. faecium-pretreated goats had lower body temperatures and fewer leukocytes than E. coli-treated goats on day 2, as well as decreased diarrhoea scores. E. coli treatment caused histopathological damage and morphological changes in the jejunum and caecum, while pretreatment with E. faecium significantly alleviated these injuries. E. faecium pretreatment can reduce the load of E. coli and increase the prevalence of Lactobacillus, thereby balancing the microbiota in the intestine. Furthermore, E. coli-infected goats pretreated with E. faecium showed obvious inhibition of Toll-like receptor 4, interleukin (IL)-1β, IL-6, IL-8 and tumour necrosis factor-α mRNA expression in the jejunum and caecum compared to that in the E. coli treatment group. In conclusion, the addition of E. faecium to goat feed is beneficial for improving clinical symptoms, maintaining intestinal mucosa integrity, balancing the microbiota and decreasing inflammatory responses in E. coli-induced intestinal injury.