Aqueous two-phase extraction (APTE) stands out as an environmentally friendly technique for the separation of metal ions. The separation of Re (VII) and Mo (VI) in an aqueous solution was investigated using a novel aqueous two-phase system (ATPS) consisting of isodecanol polyoxyethylene ether (E-1006), ammonium sulfate, and water. A phase diagram of this system was developed, and the effects of pH, temperature, extraction time, the concentrations of E-1006 and (NH4)2SO4, and metal ions on the separation of Re (VII) and Mo (VI) were examined. The results show that at pH 7.0, Mo (VI) had almost transformed into the (NH4)2SO4-rich phase, while Re (VI) was extracted into the E-1006-rich phase. The increase in temperature induces a transition of Mo (VI) to the salt-rich phase, which is unfavorable for the extraction of Re (VII). The increase in the concentrations of E-1006 and (NH4)2SO4 has a positive effect on the separation of rhenium and molybdenum. Overall, the ATPS consisting of 200 g/L of E-1006, 200 g/L of (NH4)2SO4, and water yields an extraction efficiency of 97.2% for Re and a high separation factor of 2700 for Re (VII) and Mo (VI) from a mixture of 0.1 g/L of Re (VII) and 5 g/L of Mo (VI) at pH 7.0 and 323.15 K. Separation studies of the simulated leaching solution show that the extraction efficiency for Re (VI) is 99.1% and the separation factor of Re (VII) and Mo (VI) is 5100.