Phosphate rock containing rare‐earth elements (REEs) is considered one of the most promising potential secondary sources of REEs, as evidenced by large tonnages of phosphate rock mined annually. The bioleaching of REEs from phosphate rock using Acidithiobacillus ferrooxidans was done for the first time in this study, and it was found to be greater than abiotic leaching and was more environmentally friendly. The result showed that the total leaching rate of REEs in phosphate rock was 28·46% under the condition of 1% pulp concentration and pH = 2, and the leaching rates of four key rare earths, Y, La, Ce and Nd, were 35·7, 37·03, 27·92 and 32·53% respectively. The bioleaching process was found to be accomplished by bacterial contact and Fe2+ oxidation. The blank control group which contained Fe2+ was able to leach some of the rare earths, indicating that the oxidation of Fe2+ may affect the leaching of rare earths. X‐ray diffraction analysis showed that the minerals were significantly altered and the intensity of the diffraction peaks of dolomite and apatite decreased significantly after microbial action compared to the blank control, and it was observed that bacteria adhere to the mineral surface and the minerals become smooth and angular after bioleaching by scanning electron microscope, indicating that bacteria have a further effect on the rock based on Fe2+ oxidation. Finally, Fourier transform infrared spectroscopy and three‐dimensional excitation‐emission matrix fluorescence spectra analysis showed that extracellular polymeric substances participate in the bioleaching process.