The present study examined the effects of fructooligosaccharide (FOS) supplementation in drinking water on the growth performance, carcass characteristics, hematological and biochemical parameters, antioxidant status, and cecal microbiota of New Zealand White (NZW) and APRI rabbits. A total of 180 male NZW and APRI rabbits (aged five weeks; average live body weight 700 ± 39 g) were divided into six groups (30 rabbits/group; 5 replicates/group) in a two × three factorial arrangement. Rabbits of each breed were randomly assigned to one of three treatments of FOS (control; 0.00, FOS-0.5, and FOS-1.0). Results showed that rabbits’ final body weight, FBWG, and carcass traits were considerably enhanced compared to those in the control group. The interaction effect of the supplement with the rabbit breed increased the growth, carcass traits, and hematobio-chemical and antioxidant parameters with increasing FOS levels. In the cecum of both rabbit breeds, the total bacterial count and Escherichia coli population were considerably low, with a substantial increase in the number of Lactobacilli supplemented by FOS. In conclusion, FOS supplementation enhanced growth and carcass traits by improving the hematobiochemical parameters and antioxidant status and reducing cecal pathogenic bacteria in both breeds.