This study was conducted to investigate the effects of dietary fructooligosaccharides (FOS) on the growth, survival rate, digestive enzyms activity, and the expression of intestinal barrier function genes in tropical gar (Atractosteus tropicus) larvae. A total of 960 larvae (0.030 ± 0.006 g) were fed three diets supplemented with increasing FOS concentrations (2.5, 5, and 7.5 g kg−1) and a control diet for 15 days. Results revealed that a 7.5 g kg−1 FOS supplementation improved weight gain, specific growth rate, and survival rate (p < 0.05). Furthermore, 5 g kg−1 FOS supplementation increased alkaline protease and amylase activities and induced an upregulation of the claudin-17 gene expression (p < 0.05). Meanwhile, the inclusion of 7.5 g kg−1 FOS induced the upregulation of mucin 2 (muc-2), and the tight junction genes zo-2 and claudin-3 (p < 0.05). In addition, 2.5, 5, and 7.5 g kg−1 FOS promoted the downregulation of the claudin-15 gene expression (p < 0.05). At the same time, FOS inclusion did not increase the pro-inflammatory cytokine il-8 expression. We can conclude that 7.5 g kg−1 FOS supplementation improves growth performance, survival rate, and digestive capacity, and could contribute to the reinforcement of the intestinal barrier function of Tropical gar larvae.