Apatite concentrate is an important source of phosphate and contains significant amounts of rare earth elements (REEs). In this study, the possibility of selective phosphoric acid leaching of phosphate and calcium from the Esfordi (Yazd province, Iran) apatite concentrate, containing 16.3% phosphorus, 37.1% calcium, 2.9% iron and 1.2% REEs was investigated. REEs concentrated in the leaching residue were processed using acid baking and bicarbonate precipitation methods. In the phosphoric acid leaching process, almost all the Ca and phosphate of the concentrate were leached from the concentrate, whereas only about 1% of the REEs were leached. By leaching the concentrate with 25% phosphoric acid at 90 °C and 1200 rpm, a residue containing 17.5% REEs, 4.8% phosphorus and 28.5% iron was obtained. The residue was acid baked, water leached and processed for removal of iron and recovery of REEs. Acid baking at 270 °C with acid to solid ratio of 2 (w/w) for 5 h led to 95% leaching of REEs. By increasing the pH of the leachate to 3.9, all the iron and phosphate were precipitated within 2 h. Finally, REEs were precipitated from the iron-free solution by using the bicarbonate precipitation method, and a product containing 39% of total REEs was produced. The results demonstrate that the three-stage process is an elegant method for processing of the Esfordi concentrate to produce phosphoric acid and an iron-free REE carbonate concentrate.