This work proposes a novel bioleaching process for enhancing the recovery of rare earth elements from phosphogypsum by using a co-culture of Acidithiobacillus ferrooxidans CL and Acidiphilium cryptum LT. The maximum production of organic acids (13.8 mM) was obtained when Acidiphilium cryptum LT was cultured for 5 days in advance, and then co-cultured with Acidithiobacillus ferrooxidans CL. This two-step co-culture process exhibited a significant synergistic action through the decrease in pH caused by the protons released during the formation of jarosite and organic acids produced by Acidiphilium cryptum LT. This process exhibited the highest extraction of total REEs: 84.5% of La, 39.0% of Ce, 70.7% of Nd, and 83.9% of Y from phosphogypsum under the optimum conditions. This study provides new insights into the positive role of jarosite formation in the bioleaching of non-sulfides minerals and simultaneously substantiated that the two-step co-culture process enhanced the recovery of rare earth elements from phosphogypsum.