Aim: The aim of this study was to perform an up-to-date meta-analysis of the association between the intake of dietary flavonoids and the risk of colorectal cancer. Methods: The PubMed and EMBASE databases were searched to identify eligible studies. The risk of colorectal cancer for the highest versus the lowest categories of flavonoids intake were assessed. Results: A total of 12 studies (5 cohort and 7 case-control studies) involving 17,481 cases and 740,859 controls were eligible for meta-analysis. High intake of dietary flavonols, flavones and anthocyanidins may decrease the risk of colorectal cancer; the pooled odds ratio (OR) for the highest intake compared with the lowest was 0.70 (0.54–0.90), 0.79 (0.83–0.99) and 0.78 (0.64–0.95), respectively. No association between the intake of total flavonoids, flavanones or flavan-3-ols and the risk of colorectal cancer was observed. Furthermore, the data showed that high intake of flavonols may decrease the risk of colon cancer [0.80 (0.68–0.94)] but not rectal cancer [0.93 (0.74–1.18)], while on the contrary, the intake of flavones may decrease rectal cancer risk [0.82 (0.70–0.97)] but not colon cancer risk [0.88 (0.69–1.13)]. Conclusions: The present study suggested that high intake of flavonols (such as quercetin) may reduce the risk of colon cancer, and high intake of flavones (such as apigenin) may reduce the risk of rectal cancer.