To date, bioethanol is not economically competitive. One strategy to overcome this limitation is co-producing ethanol and high value-added products as an integrated process. The results of this study demonstrated that flavonoids could be extracted from rice straw, and the flavonoids apigenin and kaempferol were detected by HPLC. Compared with untreated straw, ball-milling slightly increased the total amount of flavonoids and antioxidant activity measured by ABTS, DPPH, and FRAP assays. The saccharification step in the bioconversion of straw strongly affected the extraction of flavonoids from straw. The residue obtained after saccharification of ball-milled straw for glucose production was more suitable for flavonoid extraction than untreated and ball-milled straw. The yield of flavonoids from the residue was 1.51-fold higher than that from untreated straw. The antioxidant activity of flavonoids derived from the residue was similar to that of flavonoid-rich biomasses such as rice bran and wheat bran. More importantly, saccharification may significantly affect the conditions of flavonoid extraction. In this respect, treatment with cellulase may reduce the extraction time from 2.0 to 0.5 h and the extraction temperature from 80 to 30 degrees C. Therefore, saccharification in the bioconversion of straw may be considered as an enzyme pretreatment step for the efficient extraction of flavonoids from straw, serving as a sustainable process for straw utilization.