There has been growing interest in the role of intestinal microbiome in brain disorders. We examined whether dysbiosis can predispose to epilepsy. The study was performed in female and male Sprague‐Dawley rats. To induce dysbiosis, the rats were subjected to chronic restraint stress (two 2‐h long sessions per day, over 2 weeks). Cecal content from stressed and sham‐stressed donors was transplanted via oral gavage to recipients, in which commensal microbiota had been depleted by the antibiotics. The study included the following groups: (1) Sham stress, no microbiota transplant; (2) Stress, no microbiota transplant; (3) Sham‐stressed recipients transplanted with microbiota from sham‐stressed donors; (4) Stressed recipients transplanted with microbiota from sham‐stressed donors; (5) Sham‐stressed recipients transplanted with microbiota from stressed donors; and (6) Stressed recipients transplanted with microbiota from stressed donors. After microbiota transplant, all animals were subjected to kindling of the basolateral amygdala. Both chronic stress and microbiome transplanted from stressed to sham‐stressed subjects accelerated the progression and prolonged the duration of kindled seizures. Microbiome from sham‐stressed animals transplanted to chronically stressed rats, counteracted proepileptic effects of restraint stress. These findings directly implicate perturbations in the gut microbiome, particularly those associated with chronic stress, in the increased susceptibility to epilepsy.