Updated project metadata. Despite lacking a DNA intermediate, orthomyxoviruses complete their replication cycle in the nucleus and generate multiple transcripts through noncanonical splicing. This biology enables the slow accumulation of a subset of viral transcripts which serve as a timer to coordinate the later phases of the life cycle. Here we demonstrate that splicing is mediated by a unique structure in the RNA as revealed by Archaean L7Ae-mediated inhibition. We demonstrate that L7Ae expression inhibits influenza A virus, influenza B virus, and Salmon isavirus revealing a common strategy utilized by Orthomyxoviridae members. L7Ae-mediated inhibition of influenza A virus was lost with the generation of a splicing-independent recombinant strain and attempts to select for an escape mutant resulted in variants with significant fitness cost. As L7Ae recognizes conventional kink turns in various RNAs, these data implicate the formation of a similar structure as a shared strategy adopted by orthomyxoviruses to coordinate their replication cycle.