A model was developed to predict the synergistic effect of D2EHPA and Cyanex 302 on co-extraction of zinc and manganese. The experimental data of zinc and manganese extraction in pH range of 1–5, temperature of 23, 40 and 60 °C and different organic phase composition (D2EHPA and Cyanex 302) were used to propose correlations of distribution coefficients of zinc and manganese by multiple linear regression. The abilities of the model were examined by applying a case study on separation of zinc and manganese from spent alkaline battery by extraction. Effect of pH, temperature, extractant composition and phase volume were considered in the case study. Optimum operating conditions were determined for a multi-stage extraction column using the genetic algorithm as the optimization routine. These optimum operating conditions, including pH, extractant composition, temperature and phase volumetric ratio, were reported for an extraction unit with one, two, three and four equilibrium stages.