The purification of lipoxygenase in soybeans (richest known source) was attempted by precipitation, using polyethylene glycol, followed by aqueous two-phase extraction (ATPE). The preliminary purification by precipitation was standardized which resulted in two-fold purification. The influence of process parameters such as phase forming salt, molecular weight of phase forming polymer, tie line length, and phase volume ratio on the partitioning behavior of lipoxygenase during ATPE was investigated. The aqueous two-phase system of polyethylene glycol 6000 and ammonium sulfate, with inherent pH of 5.2, was found to be most suitable. The tie line length of 41.25% and volume ratio of 1.7 have resulted in 125% activity recovery with the overall purification factor of 4.38 compared to crude enzyme extract.