Efficient methods for conjugating proteins to RNA are needed for RNA delivery, imaging, editing, interactome mapping, and barcoding applications. Noncovalent coupling strategies using viral RNA binding proteins such as MS2/MCP have been widely applied but are limited by tag size, sensitivity, and dissociation over time. We took inspiration from a sequence-specific, covalent protein-DNA conjugation method based on the Rep nickase of a porcine circovirus called "HUH tag". Though wild-type HUH protein has no detectable activity toward an RNA probe, we engineered an RNA-reactive variant, called "rHUH", through 7 generations of yeast display-based directed evolution. Our 13.4 kD rHUH has 12 mutations relative to HUH and forms a covalent tyrosine-phosphate ester linkage with a 10-nucleotide RNA recognition sequence ("rRS") within minutes. We engineered the sensitivity down to 1 nM of target RNA, shifted the metal ion requirement from Mn