Burdock roots contain high contents of fructooligosaccharides and phenolic compounds; however its use as ingredient in food products is limited. This study aimed to obtain burdock root flour (BRF) by conventional drying and evaluate its potential as a prebiotic ingredient in cookies. Cookies were manufactured using a blend of whole wheat flour and refined wheat flour (51:49), replacing the concentration of refined wheat flour by BRF at 0 (C0), 5 (C1), and 10% (C2). BRF presented 40.16 g × 100 g−1 of total dietary fiber, 181.74 mg × 100 g−1 of chlorogenic acid, 6.19 g × 100 g−1 of total fructooligosaccharides (FOS), and in vitro prebiotic activity. The cookies C1 and C2 exhibited 2.2 and 4.94% (on a dry basis) of BRF, respectively, with similar (p > .05) physicochemical and technological properties, except for hardness of C1 (24.83 N), which was higher (p < .05) than C0 and C2. BRF significantly increased (p < .05) FOS in cookies from 42.38 (C0) to 366.68 mg × 100 g−1 (C2). Cookies with 4.94% BRF had a positive effect (p < .05) on the prebiotic activity. Burdock roots may be an effective alternative to provide prebiotic oligosaccharides to bakery products for consumers who search for functional foods with health benefits.