This is the first investigation, conducted in a completely randomized design (CRD), to determine the effects of different salinity levels (75 and 150 mM) and germination periods (3, 4, and 5 days) on momilactone and phenolic accumulations in germinated brown rice (GBR) var. Koshihikari. Particularly, the identification of bioactive compounds was confirmed using electrospray ionization-mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) spectroscopy (1H and13C). Momilactone A (MA) and momilactone B (MB) amounts were determined by ultra-performance liquid chromatography–electrospray ionization-mass spectrometry (UPLC–ESI-MS), whereas other compounds were quantified by spectrophotometry and high-performance liquid chromatography (HPLC). Accordingly, GBR under B2 treatment (75 mM salinity for 4 days) showed the greatest total phenolic and flavonoid contents (14.50 mg gallic acid and 11.06 mg rutin equivalents, respectively, per g dry weight). GBR treated with B2 also accumulated the highest quantities of MA, MB,ρ-coumaric, ferulic, cinnamic, salicylic acids, and tricin (18.94, 41.00, 93.77, 139.03, 46.05, 596.26, and 107.63 µg/g DW, respectively), which were consistent with the strongest antiradical activities in DPPH and ABTS assays (IC50= 1.58 and 1.78 mg/mL, respectively). These findings have implications for promoting the value of GBR consumption and rice-based products that benefit human health.