Free radical-induced oxidative stress is the root cause of many diseases, such as diabetes, stress and cardiovascular diseases. The objective of this research was to screen GABA levels, antioxidant activities and bioactive compounds in brown rice. In this study, we first fermented brown rice with different lactic acid bacteria (LABs), and the best LAB was selected based on the levels of GABA in the fermentate. Lactobacillus reuterii generated the highest levels of GABA after fermentation. To ascertain whether germination can improve the GABA levels of brown rice, we compared the levels of GABA in raw brown rice (Raw), germinated brown rice (Germ), fermented brown rice (Ferm) and fermented-germinated brown rice (G+F) to identify the best approach. Then, antioxidant activities were investigated for Raw BR, Germ BR, Ferm BR and G+F BR. Antioxidant activity was calculated using a 2,2-diphenyl-1-picryl hydrazile radical assay, 2,2-azino-bis-(3-ethylene benzothiozoline-6-sulfonic acid) radical assay and ferric-reducing antioxidant power. In Ferm BR, DPPH (114.40 ± 0.66), ABTS (130.52 ± 0.97) and FRAP (111.16 ± 1.83) mg Trolox equivalent 100g, dry weight (DW), were observed as the highest among all samples. Total phenolic content (97.13 ± 0.59) and total flavonoids contents (79.62 ± 1.33) mg GAE/100 g and catechin equivalent/100 g, DW, were also found to be highest in fermented BR. Furthermore, an untargeted metabolomics approach using ultra-high-performance liquid tandem chromatography quadrupole time of flight mass spectrometry revealed the abundance of bioactive compounds in fermented BR, such as GABA, tryptophan, coumaric acid, L-ascorbic acid, linoleic acid, β-carotenol, eugenol, 6-gingerol, etc., as well as bioactive peptides which could contribute to the health-promoting properties of L. reuterii fermented brown rice.