Organic acids have recently been identified as promising replacements for antibiotics in aquafeeds that promote fish growth and feed efficiency. This study evaluated the inclusion of fumaric acid (FA; 0, 5, 10, 15, 20, and 30 g/kg) in diets (350 g/kg CP; 3.4 kcal digestible energy/g) of Nile tilapia juveniles. Fish (average weight 1.7 ± 0.1 g) were distributed in three 40 L aquaria per treatment (13 fish/aquaria) in a completely randomized design. Over 35 days, the fish received the experimental diets three times daily to apparent satiety. The maximum weight gain, feed efficiency ratio, and protein efficiency ratio were recorded in fish supplemented with 14–15 g/kg FA. After 28 days, Enterobacteriaceae was registered only in the gut of tilapia without FA augmentation. Gram-negative bacteria in the fish gut decreased (p < 0.05) in fish receiving 17 g/kg of dietary FA, increased after this level. The intestinal villi height and width were affected (p < 0.05) by FA levels and feeding time. Thus, inclusion of 15 g/kg of FA was effective in promoting growth, improving intestinal morphometry, and decreasing negative gut bacteria of Nile tilapia juveniles after 35 days.