Buckwheat is well-known as a healthy crop with excellent nutritional and functional superiority mainly because of a high content of flavonoid compounds, specifically, rutin. However, buckwheat-based food products are known to have the reduced levels of rutin by rutin-degrading enzymes that generate quercetin during processing. However, since quercetin has a bitter taste, it may have a negative impact on consumer preferences, consequently retarding the utilization of buckwheat flour to a variety of buckwheat processed foods. Thus, this study was carried out to investigate the levels of rutin and quercetin in the milling fractions of buckwheat flours and also to monitor their changes by a variety of thermal treatments. Native buckwheat was separated into three fractions by sieving with 40 and 100 mesh screens which were designated as >40 M, 40-100 M, and 100 M<, respectively. The levels of rutin were the highest in the 40-100 M milling fraction, followed by <100 M and >40 M. Also, buckwheat flours were subjected to several thermal treatments including steaming and autoclaving. The contents of rutin and quercetin in the resulting buckwheat samples were analyzed by HPLC and the correlations between the flavonoid compounds and thermal treatments were investigated. The addition of water to buckwheat flour in making buckwheat products significantly decreased the levels of rutin while the quercetin content increased. However, the thermal treatments of buckwheat flours distinctly reduced the rutin loss and quercetin was hardly detected. Therefore, this study contributes to enhancing the health functionalities of buckwheat by reducing rutin loss, probably extending use of buckwheat flour to a variety of processed food products.