A pilot-scale (120L) bioreactor system using a gel carrier-entrapped pure bacterial strain, Afipia sp. strain D1, capable of degrading 1,4-dioxane as a sole carbon and energy source was constructed and applied to treat real industrial wastewater containing 1,4-dioxane from a chemical factory. Although the wastewater not only contained high concentrations of 1,4-dioxane but also considerable amounts of other organic compounds (73mg-TOCL−1 on average), the bioreactor could efficiently remove 1,4-dioxane without significant inhibitory effects. The reactor startup could be completed within approximately 1 month by increasing the 1,4-dioxane loading rate (0.09–0.47kg-dioxanem−3d−1) in a stepwise manner. Effective 1,4-dioxane removal was stably maintained for 3 months with an influent 1,4-dioxane of 570–730mgL−1, giving an average effluent concentration and removal rate of 3.4mgL−1 and 0.46kg-dioxanem−3d−1, respectively. A 1,4-dioxane loading fluctuation between 0.14 and 0.72kg-dioxanem−3d−1 did not significantly affect its removal, and more than 99% removal efficiency was constantly maintained. The Monod model could well describe the relationship between the effluent 1,4-dioxane concentration and 1,4-dioxane removal rates of the bioreactors, showing that the half-saturation constant (Ks) was 28mgL−1.