Fuel reduction treatments are used to reduce wildfire risk and to restore plant communities. Yet, repeated mechanical or prescribed fire treatments may gradually change forest structure and microhabitat conditions, favoring some taxa and decreasing suitability for others. We experimentally assessed long‐term (intermittent years, 2003–2016) effects of repeated dormant‐season mechanical and prescribed fire treatments on capture rates of reptiles and amphibians in southern Appalachian upland hardwood forests. Treatments were mechanical understory removal (twice), prescribed burning (4 times; burn‐only), mechanical understory removal followed 1 year later by high‐severity prescribed burns and 3 subsequent burns (mechanical + burn), and untreated controls. Initial burns were hotter in mechanical + burn than burn‐only units, resulting in heavy tree mortality and increased canopy openness within 2 growing‐seasons post‐burn. We captured 4,606 individuals of 15 amphibian and 20 reptile species. Capture rates of American toads (Anaxyrus americanus), green frogs (Lithobates clamitans), plethodontid salamanders (Plethodon spp.), and northern red salamanders (Pseudotriton ruber) were not affected by any fuel reduction treatment. The capture rate of five‐lined skinks (Plestiodon fasciatus) was greater in mechanical + burn than burn‐only or control units, and the capture rate of eastern fence lizards (Sceloporus undulatus) was greater in mechanical + burn than control units. Juvenile eastern fence lizard captures were greater in mechanical + burn units and increased over time, indicating that high‐severity burning followed by repeated burns may improve conditions for successful recruitment. Different responses among species highlight the importance of including multiple taxa when assessing effects of forest disturbances on wildlife, and give perspective on how forest health may vary depending on target taxa.