When DNA replication is challenged cells activate a DNA synthesis checkpoint, blocking cell cycle progression until they are able to overcome the replication defects. In fission yeast, Cds1 is the effector kinase of this checkpoint, inhibiting M‐phase entry, stabilizing stalled replication forks and triggering transcriptional activation of S‐phase genes. The molecular basis of this last effect is largely unknown. The Mlu1 binding factor (MBF) complex controls the transcription of S‐phase genes. We purified novel interactors of the MBF complex and identified the repressor Yox1. When the DNA synthesis checkpoint is activated, Yox1 is phosphorylated, which abrogates its binding to MBF. MBF‐dependent transcription therefore remains active until cells are able to overcome this challenge.