Nuclear export of mRNA is extensively coupled to transcription and processing of mRNA throughout the cell cycle. Little is known about how cells regulate mRNA export during DNA replication in S-phase. Here, we uncover a checkpoint mediated by WEE1, CDK1 and PLK1 that regulates mRNA export in response to replication stress. We show that mRNA export complexes are recruited to sites of replication stress in S-phase. WEE1 inhibition prematurely activates CDK1 and PLK1, leading to accumulation of R-loop associated mRNA in large nuclear speckles, with late markers of replication stress present around their periphery. This recruitment is dependent on CDK1 activity. Phosphorylation of ALYREF by CDK1 and PLK1 regulates nuclear speckle accumulation of mRNA following replication stress. mRNA export factors including ALYREF are subsequently mis-localised from these speckles, preventing nuclear export of R-loop associated mRNA. Thus, WEE1, CDK1 and PLK1 enforce a cell cycle checkpoint that serves to protect the cell from major sources of genome instability by ensuring that R-loop associated mature mRNA is not exported to the cytoplasm.