The present study has applied acid-based deep eutectic solvent containing choline chloride with malonic, malic, tartaric, and citric acids for ultrasound-assisted extraction of bioactive compounds from Empetrum hermafroditum Hager. Kinetics of the extraction process has been estimated in the framework of the second-order and film theory models obtaining time dependence of total phenolic compound yield and total flavonoid yield using Folin-Ciocalteu and AlCl3-complexation methods. Total antioxidant activity of extracts has been estimated using the phosphomolybdate method and DPPH radical assay. HPLC has determined that quercetin and kaempferol were present in the extracts. Temperature, time, and water addition to deep eutectic solvents (DESs) have been optimized for the extraction process using the Box-Behnken design. The optimal conditions for the extraction of polyphenolic compounds are 3 h at 45 °C with the addition of 50% water. Polyphenol yield achieves 320.8 mg mL−1. The optimal conditions for flavonoid extraction are 5 h at 60 °C with the addition of 30% water. Total flavonoid yield achieves 58.8 mg mL−1. Obtained data demonstrate DESs as promising extractants for bioactive component recovery from Empetrum hermafroditum Hager.