Here, we report an iron-catalyzed cross-coupling reaction of electron-deficient heterocycles and quinone with organoboron species via innate C-H functionalization. Iron(II) acetylacetonate along with oxidant (K2S2O8) and phase-transfer catalyst (TBAB) under open flask conditions efficiently catalyzed the cross-coupling of pyrazine with arylboronic acids and gave monoarylated products in good to excellent yields. Optimized conditions also worked for other heterocylces such as quinoxalines, pyridines, quinoline, and isoquinoline as well as quinones. In addition, we demonstrated as a first example its application for the synthesis of anticancer marine pyrazine alkaloid botryllazine A.