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Penaeus spp. are the most cultivated type of shrimp because they have rapid growth and good adaptation to farming conditions. Due to diseases that result in high mortality and a decreased product quality, the cultivation of these shrimp globally, and in Cuba in particular, comes with the risk of significant financial losses. This study examined the effect of fructooligosaccharide (FOS, 1-kestose) on the growth and immune response of shrimp, as well as the multitude of Vibrio spp. and Pseudomonas spp. in Penaeus vannamei post-larvae under culture conditions. Fructooligosaccharide was applied in a completely randomized manner at a concentration of 0.4%, in both experimental groups with seventeen tanks each. In the results of this investigation, animals of greater weight (control 6.8 ± 0.2 mg; FOS 9.5 ± 0.3 mg; p < 0.001), length (control 1.1 ± 0.1 mm; FOS 1.3 ± 0.1 mm; p < 0.001), and survival (control 61.7% (95% CI of median 54.2–70.0); FOS 76.6% (95% CI of median 72.1–84.2); p < 0.001) were obtained when administered FOS relative to the control. An increase in the activity of proteases (p < 0.001), enzymes of the innate immune system such as phenoloxidase (p < 0.001), and lysozymes (p < 0.001) was observed, as well as an increase in the number of lectins (p < 0.001). Changes in the microbiota could be observed, with a reduction in Vibrio spp. and Pseudomonas spp. (control 2.4 × 103 ± 0.5 × 103; FOS 1.1 × 102 ± 0.3 × 102; p < 0.001). FOS improves the quality of the post-larvae of P. vannamei as reflected in the length, weight, and survival of the animals. Moreover, FOS stimulates the P. vannamei immune system through the enzymatic activities of phenoloxidase, lysozyme, and a number of lectins. The reduction in the population load of Vibrio spp. and Pseudomonas spp. might be a consequence of the improvement in the quality and immune system of P. vannamei.