Absolute reduction of perchlorate has proven complex owing to the diverse characteristics of the perchlorate ion. Technologies such as chemical reduction, ozone/peroxide, nanofiltration, and reverse osmosis have had limited success, high costs and are not environmentally friendly. A great deal of research and reviews on ion exchange and biodegradation have been carried out, but conditions for optimal biodegradation are not yet well understood. The acceptability of biological treatment of perchlorate has been limited due to challenges such as electron donor availability, which impacts on the environmental sustainability of perchlorate biodegradation, the biomass inventory, secondary contamination of treated water due to contact with micro-organisms between the treatment unit and the final effluent, and the presence of other energetic compounds such as Royal Demolition Explosives and 2,4-dinitroanisole (DNAN) in army PAX 21 production water and other competing electron acceptors such as nitrate and sulfate. Therefore, the current research concern is about optimization of the biodegradation of perchlorate for large-scale applicability. In addition to summarizing the strengths and weaknesses of developed and emerging perchlorate treatment technologies, this review focuses on research developments in biological treatment of ammonium perchlorate, perchlorate reducing bacteria, factors affecting biodegradation of NH4 ClO4− and previous research recommendations on efficient, effective, and stable biological treatment of perchlorate-contaminated wastewater.