Constipation affects around 30% of children and in 95% of cases is functional (FC), a consequence of alterations in digestive tract peristalsis, modulated by the immune and nervous systems, bile acid metabolism, and the gut microbiota. The aim of this review was to assess the role of gut microbiota and the use of probiotics in children with constipation. The current treatment involves education, toilet training, and oral laxatives, effective in only 50% of patients. In chronic FC, the composition of the microbiota is altered, with increased abundance of Bacteroidetes, Enterobacteriaceae, and Firmicutes and decreases in Prevotella, Bifidobacteria, Faecalibacterium prausnitzii, and Clostridium leptum. Probiotics replenish lacking beneficial resident bacteria, downregulate mucosal inflammation, or produce short-chain fatty acids (SCFAs). Probiotics like Bifidobacterium breve and Bifidobacterium longum increase the defecation frequency and decrease the episodes of both fecal incontinence and abdominal pain. Bifidobacterium animalis subsp. lactis XLTG11 improves the gut microbiota by upregulating SCFA genes and downregulating those related to methane metabolism. Lactobacilli produce organic acids that stimulate bowel peristalsis and augment fecal bolus moisture. The heterogeneity of the current studies involving pediatric subjects thus far hinders the use of probiotics as a standard in the management of children with constipation.