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This study focused on optimizing ultrasound-assisted extraction (UAE) conditions (<i>X_PC</i>: pulse cycle of 1:1, 2:1, and 3:1 s on/off; <i>X_UP</i>: ultrasound power of 80, 90, and 100%; and <i>X_ET</i>: extraction time of 2, 4, and 6 min) for maximizing the content of soluble phenols (TSPs) and flavonoids (FLAs) from a native Mexican pigmented corn kernel powder through response surface methodology (RSM). Under the Box–Behnken design conditions, the UAE of TSPs ranged from 27.72 to 34.87 mg/g, while FLA content ranged from 16.59 to 27.28 mg/g. The highest content for TSPs was under 4 min <i>X_ET</i>, 1:1 s on/off <i>X_PC</i>, and 100% <i>X_UP</i>, while for flavonoids it was under 6 min <i>X_ET</i>, 2:1 s on/off <i>X_PC</i>, and 80% <i>X_UP</i>. According to RSM analysis, the optimal UAE conditions for TSPs were found to be <i>X_ET</i> 3.15 min, 1.58 s on/off <i>X_PC</i>, and 100% <i>X_UP</i>, and an <i>X_ET</i> of 4.18 min, 3 s on/off <i>X_PC</i>, and 80% <i>X_UP</i> were the best experimental conditions for FLAs with a predictive TSP of 35.07 mg/g and FLA of 27.51 mg/g. These data were adjusted in a second-order polynomial model and experimentally validated (TSP = 34.06 mg/g and 27.04 mg/g). Furthermore, the extracts demonstrated antioxidant activity (ABTS, FRAP, and DPPH methods) for optimal UAE for TSPs and FLAs. The antioxidant extract from the native Mexican pigmented corn kernel powder can be used for diverse industrial applications. Thus, the UAE is an effective and sustainable technology for recovering bioactive compounds from maize-based materials.