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This is the first study aiming to enrich momilactones A (MA) and B (MB) and phenolic compounds in germinated brown rice (GBR) and non-GBR var. Koshihikari and Milky Queen through the cooking process. Extraction methods for these compounds were optimized by applying various conditions, including solvents (80% methanol and 80% ethanol), heat (80 °C), and sonication (2 h). Momilactone and phenolic quantities were determined by ultra-performance liquid chromatography–electrospray ionization mass spectrometry (UPLC–ESI-MS) and high-performance liquid chromatography (HPLC), respectively. Accordingly, cooked Koshihikari GBR extract using 80% methanol and sonication (GKB4) revealed the highest amounts of tricin, caffeic, <i>ρ</i>-hydroxybenzoic, <i>ρ</i>-coumaric, ferulic, salicylic, and cinnamic acids (1.71, 1.01, 0.62, 0.45, 0.94, 2.50, and 0.37 mg/g DW, respectively), consistent with the strongest antiradical activities in DPPH and ABTS assays (IC₅₀ = 1.47 and 1.70 mg/mL, respectively). Non-cooked GBR Koshihikari extract using 80% ethanol and sonication (GKB9) exhibited the highest MA and MB contents (147.73 and 118.8 μg/g DW, respectively). Notably, GKB9 showed potent inhibition of α-amylase and α-glucosidase (IC₅₀ = 0.48 and 0.15 mg/mL, respectively), compared with the anti-diabetic drug acarbose (IC₅₀ = 0.26 and 2.48 mg/mL, respectively). The findings hold significant implications for developing phenolic- and momilactone-enriched brown rice with health-beneficial properties.