The early cell divisions of many metazoan embryos are rapid and occur in the near absence of transcription. At the mid-blastula transition (MBT) the cell cycle elongates and several processes become established including the onset of bulk transcription and cell cycle checkpoints. How these events are timed and coordinated is poorly understood. Here we show in Xenopus laevis that developmental activation of the checkpoint kinase Chk1 at the MBT results in the SCFβ-TRCP-dependent degradation of a limiting replication initiation factor Drf1. Inhibition of Drf1 is the primary mechanism by which Chk1 blocks cell cycle progression in the early embryo and is an essential function of Chk1 at the blastula to gastrula stage of development. This study defines the down-regulation of Drf1 as an important mechanism to coordinate the lengthening of the cell cycle and subsequent developmental processes.