Perturbations of the gastrointestinal (GI) microbiota (i.e. dysbiosis) in early life may induce vulnerability of the enteric nervous system (ENS), contributing to early onset GI disorders, such as irritable bowel syndrome (IBS). Probiotics, such as Lacticaseibacillus rhamnosus GG (LGG), may improve pediatric digestive disorders; however, the mechanisms involved, including effects on the ENS, are not yet fully understood. In this study, the long-lasting consequences of antibiotic-induced dysbiosis on intestinal neuromuscular function, as well as the effect of LGG, were evaluated in juvenile female and male mice. One week after antibiotic treatment cessation, broad-spectrum antibiotic treatment induced significant taxonomic changes in both sexes compared to untreated control animals. These changes appeared earlier and involved more potentially harmful bacterial taxa in females than in males. LGG effectively prevented alterations in microbial communities in both sexes, with a more pronounced protective effect in males. Dysbiosis reduced transit efficiency, nitrergic relaxations, and tachykinergic contractions only in females, with no significant effect of LGG in this group. In both sexes, dysbiosis decreased cholinergic contractions; however, LGG restored the excitatory responses to control levels only in males. In summary, early antibiotic-induced dysbiosis in juvenile mice leads to persistent effects during late adolescence on both gut microbiota composition and neuromuscular function. These alterations are more pronounced and less responsive to LGG treatment in females. The findings underscore the critical role of the enteric microbiota in early-life development of functional gastrointestinal disorders with sex-specific features, such IBS.