Enteropathogenic Escherichia coli (EPEC) is one of the etiological agents that causes diarrhea in weaning pigs. In this study, we report that mutating both relA and spoT genes in EPEC E2348/69 can promote bacterial clearance in porcine gastrointestinal tract (GIT). Our experimental analyses showed that an E2348/69 ΔrelAΔspoT mutant strain was not detected in porcine feces after 1 day post-infection (dpi), whereas its parental strain was continuously detected in porcine feces within 10 dpi. Histologic assessment revealed that the mutant strain was unable to induce moderate pathologic lesions in porcine GIT when compared to those with the wildtype strain. Taken together, our data suggest that the relA and spoT genes in EPEC play an important role in bacterial survival and pathogenesis in porcine GIT.