Mustard bran is enriched with bioactive phenolic compounds and glucosinolates, yet it is underutilized as a low-value processing by-product. Here, we investigate the effects of solid-state fermentation (SSF) using various food-grade microorganisms (Aspergillus spp., Rhizopus spp., Bacillus subtilis, Saccharomyces cerevisiae) on the phytochemical composition and antioxidant activities of oriental mustard and yellow mustard brans. The total phenolic contents (TPC) and antioxidant activities (FRAP, DPPH assays) of oriental and yellow mustard brans were significantly improved (p < 0.05) after fermentation, especially by R. oligosporus and R. oryzae. Moreover, SSF by R. oligosporus and R. oryzae significantly increased (p < 0.05) the levels of p-hydroxybenzoic acid, syringic acid, protocatechuic acid, sinapic acid and kaempferol-3-O-glucoside in both mustard brans. Conversely, a significant reduction (p < 0.05) of major glucosinolates in oriental and yellow mustard brans were observed after SSF by R. oligosporus. Findings from this study show that SSF by filamentous fungi is a promising strategy to enhance the phenolic contents, antioxidant properties and overall value of oriental and yellow mustard brans.