The aim of this systematic review and meta-analysis was to assess the effects of β-fructan supplementation on bowel function in healthy volunteers and patients. The search process was based on the selection of publications listed in the Pubmed and EUPMC database until December 2017, plus two unpublished studies, to identify studies evaluating the impact of β-fructans on bowel movement and stool parameters. Forty-seven publications were selected for inclusion. Primary parameter was frequency of bowel movements, evaluated by the number of defecations per day during the study period. Secondary outcomes were stool consistency, stool dry and wet weights, and transit time. Short-chain (DP < 10) β-fructans contributed to increased stool frequency (0.36 defecation +/− 0.06 per day; p < 0.001), while no significant effect was reported with long-chain (DP ≥ 10) β-fructans (−0.03 +/− 0.11, p = 0.82). A minimal increase in stool wet weight was also statistically demonstrated with short-chain β-fructans. Moreover, the meta-analysis highlighted significant differences in stool consistency in contrast to fecal dry weight after β-fructan supplementation. This systematic review and meta-analysis indicates that short-chain β-fructan supplementation has a positive effect on bowel function by significantly increasing the frequency of bowel movements.