In children, diseases like asthma, juvenile arthritis, type 1 diabetes, Crohn’s disease, and mental disorder have been linked to antibiotics. There can be a link between basic mechanisms and gut microbiome dysbiosis. The link between antibiotics and alteration of the pediatric gut microbiota was analyzed. MEDLINE, EMBASE, and Web of Science were used in the searches. Studies investigating the relationship between antibiotics and gut microbiome dysbiosis; children aged 0 to 18 years; molecular methodologies of assessment; microbiome richness, diversity, or composition outcomes were all eligible. The Newcastle–Ottawa Scale or the Cochrane Risk of Bias Tool were used to assess quality. Meta-analysis was viable. There were a total of 4,668 papers found, with 12 in the final analysis (5 RCTs, 5 cohort studies, and 2 cross-sectional studies). Three studies looked at microbiome richness, species diversity in 6, and species composition at 10. The evidence was of good or acceptable quality. A substantial decrease in diversity and decrease in richness was found in 5 and 3 studies respectively. For twice as long as penicillin, macrolide exposure and lower richness were linked. Proteobacteria like E. coli showed considerable increases (4 studies), while Bifidobacteria (5 studies) and Lactobacillus (2 studies) showed large reductions. A significant decrease in alpha-diversity (Shannon index: mean difference -0.86 (95% CI -1.59, -0.13) was found by a meta-analysis of RCTs on the effect of macrolide (azithromycin) exposure on the gut microbiome. There was a link between antibiotic exposure and decreased microbiome diversity and richness, as well as bacterial abundance alterations. Antibiotic exposure was linked to decreased microbiome diversity and richness, as well as bacterial abundance alterations. When prescribing antibiotics for children, the risk of dysbiosis in the microbiome should be considered.