Flavor is one of the important factors for udon, white salted Japanese noodles that are produced by mixing flour, salt, and water prior to being shaped and boiled. Using dynamic headspace extraction-gas chromatography/mass spectrometry, we analyzed the volatile compounds emitted from the flour, dough, and boiled noodles to clarify the formation mechanism of the udon flavor. The volatile compound profiles were analyzed by principal component analysis; those from the dough and noodles were compared to those from the flour. Hydrocarbons were the main compounds emitted from the flour, and aldehydes and ketones from the dough and noodle. These aldehydes and ketones were presumed to be generated from the enzymatic oxidation of unsaturated fatty acids by lipoxygenase (LOX) upon the addition of water. Notably, the abundances of aldehydes and ketones increased during the noodle-making process, affecting the volatile compound profiles of the noodles. Noodles prepared from Nourin 61 flour, which are preferred by consumers, had higher contents of aldehydes and ketones and higher LOX activity. Therefore, the unique volatile compound profiles of udon may be generated by the LOX activity in wheat flour, and these aldehydes and ketones may contribute to the characteristic udon flavor.