Rare earth elements (REEs) are of great importance to modern society and their reliable supply is a major concern of many industries that utilize them in metal alloys, semiconductors, electrical equipment, and defense equipment. REEs in the coal waste have been revealed to be an alternative resource for REEs production. In this study, the extraction, recovery, and upgrading of the REEs from coal waste has been realized with the bioleaching and precipitation processes. Reliable and sustainable acid and oxidant production from the oxidation of the pyrite with Acidithiobacillus ferrooxidans to generate acid for leaching were realized in this research. The acidified bioleaching solution was used to extract REEs from coal waste, with 13–14% yields for most REE elements (~72 h of leaching). However, recovery for longer duration tests was significant higher (varies from 40–60% for individual REEs). After extraction, precipitation and separation processes were designed with the aid of Visual Minteq calculations and modeling to concentrate the REEs. With the procedures designed in this research, a final REEs precipitate product containing 36.7% REEs was produced.