Trl1 is a well-characterized factor with RNA kinase (KIN), cyclic phosphodiesterase activity (CDP), and ligase activities (LIG) essential for tRNA processing. Indeed, splicing of tRNAs is known to generate 5’OH-intronic RNAs, which require Trl1 kinase activity to permit their degradation by Xrn1. Here we show that its RNA kinase activity is not limited to tRNA splicing and NGD-targeted mRNAs but also degrades the majority of 5’-hydroxylated RNA species present in the cell. The importance and cellular advantage of such RNA kinase activity are discussed.