High-rate activated sludge (HRAS) systems are designed to shift the energy-intensive processes to energy-saving and sustainable technologies for wastewater treatment. The high food-to-microorganism (F/M) ratios and low solid retention times (SRTs) and hydraulic retention times (HRTs) applied in HRAS systems result in the maximization of organic matter diversion to the sludge which can produce large amounts of biogas during anaerobic digestion, thus moving toward energy-neutral (or positive) treatment processes. However, in addition to the energy optimization, the removal of emerging contaminants (ECs) is the new challenge in wastewater treatment. In the context of this study, the removal efficiencies and the fates of selected ECs (three endocrine disruptors (endocrine disrupting chemicals (EDCs))—nonylphenol, bisphenol A and triclosan, and four pharmaceuticals (PhACs)—ibuprofen, naproxen, diclofenac and ketoprofen) in HRAS systems have been studied. According to the results, EDCs occurred in raw wastewater and secondary sludge at higher concentrations compared to PhACs. In HRAS operating schemes, all compounds were poorly (<40%) to moderately (<60%) removed. Regarding removal mechanisms, biotransformation was found to be the dominant process for PhACs, while for EDCs sorption onto sludge is the most significant removal mechanism affecting their fates and their presence in excess sludge.