The authors show that CKS proteins stimulate the CDK2-mediated phosphorylation of Treslin in a non-canonical fashion, rather by stabilizing the interaction between CDK2 and Treslin. CKS proteins are important for the assembly of an active replicative helicase in response to the intra S-phase checkpoint. The levels of CKS proteins increase during recovery from replication stress and this increase is necessary for the recovery. Together these results define a new role of CKS protein in regulating the replication stress checkpoint.