In this investigation, bioleaching of vanadium from uranium ore residue of the leaching stage was studied by Aspergillus niger in a two-step process at 30 °C and 150 rpm. The first step was initiated by growth of fungi in the absence of mine waste. Using response surface methodology, three factors were surveyed for fungal growth: initial pH, sucrose concentration and spore population. Also concentrations of oxalic, citric, and gluconic acids were measured as response in this step. During 30 days, maximum productions of these acids were 3265, 11578, and 7988 mg/l, respectively. Initial pH and sucrose concentration were significant factors for oxalic and citric acid production; however, for gluconic acid production sucrose concentration and spore population were significant. Then, the content of each flask was filtered and mine waste was added to liquor with pulp density of 3%. During 3 days, in the second step, vanadium recovered about 44.8% in the liquor.