Foxtail millet husk (FMH) is generally removed and discarded during the first step of millet processing. This study aimed to optimize a method using deep eutectic solvents (DESs) combined with ultrasonic-assisted extraction (UAE) to extract phenols from FMH and to identify the phenolic compositions and evaluate the biological activities. The optimized DES comprised L-lactic acid and glycol with a 1:2 molar ratio by taking the total flavonoid content (TFC) and total phenolic content (TPC) as targets. The extraction parameters were optimized to maximize TFC and TPC, using the following settings: liquid-to-solid ratio of 25 mL/g, DES with water content of 15%, extraction time of 41 min and temperature of 51 °C, and ultrasonic power at 304 W. The optimized UAE-DES, which produced significantly higher TPC, TFC, antioxidant activity, α-glucosidase, and acetylcholinesterase inhibitory activities compared to conventional solvent extraction. Through UPLC–MS, 12 phenolic compounds were identified, with 1-O-p-coumaroylglycerol, apigenin-C-pentosyl-C-hexoside, and 1-O-feruloyl-3-O-p-coumaroylglycerol being the main phenolic components. 1-O-feruloyl-3-O-p-coumaroylglycerol and 3,7-dimethylquercetin were identified first in foxtail millet. Our results indicated that FMH could be exploited by UAE-DES extraction as a useful source of naturally derived antioxidants, along with acetylcholinesterase and α-glucosidase inhibitory activities.