Germinated wheat is a food material with potential health benefits due to its high phenolic and antioxidant content, but the reason why germination increases this content is unclear. The aim of this study was to investigate the relationships between protein changes (determined by two-dimensional gel electrophoresis (2-DE)), phenolics, γ-aminobutyric acid (GABA) levels, and antioxidant capacity of wheat germinated for various periods (24, 48, 72, and 96 h) compared to control. Each phenolic acid tended to increase with increasing germination time. The GABA content was highest (39.98 mg/100 g dwb) after 96 h of germination. The total oxygen radical absorbance capacity (ORAC) was 1.97 times higher after 96 h than in ungerminated seeds. Fifteen proteins, among 82 proteins separated by 2-DE, were highly related with ORAC and were identified by peptide mass fingerprinting (PMS). The PMS revealed strong expression of granule bound starch synthase (GBSS) and glutathione S-transferase (GSTF) after 96 h of germination. Overall, the ORAC at 96 h exhibited a close relationship with the levels of phenolic acids, GABA, and proteins such as GBSS and GSTF. In conclusion, these findings add to the existing knowledge of wheat protein changes and their relationship to the antioxidant properties of germinating wheat seeds.