Circadian rhythm disruption is intimately linked to atherosclerosis, and endothelial-to-mesenchymal transition (EndMT) is a major feature of atherosclerosis progression and unstable plaques. However, the mechanisms underlying the roles of Brain and Muscle ARNT-Like Protein-1 (BMAL1), an essential clock transcription activator, in EndMT and plaque instability have not been characterized. In the present study, we found a positive relationship among BMAL1 expression loss, EndMT, and plaque vulnerability in human carotid plaques. Furthermore, loss-and gain-of-function studies in human aortic endothelial cells (HAECs) revealed that BMAL1 inhibited oxidized low-density lipoprotein (oxLDL)-induced intracellular reactive oxygen species (ROS) accumulation and subsequent EndMT. Mechanistically, BMAL1 deficiency aggravated EndMT through BMP-mediated signaling. Collectively, our study demonstrates the underlying mechanism for the central role of BMAL1 loss in atherosclerosis progression and plaque stability transition promoted by oxidative stress, which can be targeted therapeutically to prevent the occurrence and progression of atherosclerosis.