Background <p>Zika virus (ZIKV) is a mosquito-borne Flavivirus with a strong affinity for the central nervous system (CNS). After infection, ZIKV can cross the blood-brain barrier (BBB) and reach the CNS, causing potential harm to both adult and developing brains.</p> Methods <p>The current study aims to evaluate how dysregulated circadian rhythms can affect brain infection by ZIKV, as biorhythms regulate essential physiological processes and disrupted circadian clock can contribute to the pathogenesis of multiple disorders. Both ZIKV infection and circadian rhythm alterations have been related to the disruption of the BBB integrity by modulating the expression of the tight junction (TJ) proteins, however, the input of circadian misalignment on ZIKV infection has never been studied in the literature.</p> Results <p>Infection of brain endothelial cells with ZIKV selectively impacted endothelial permeability and dysregulated the expression of TJ and mitochondrial proteins. Importantly, these effects were potentiated by silencing <i>Bmal1</i>, a critical circadian rhythm gene. These results were then confirmed in vivo in <i>Bmal1</i> endothelial cell-specific knockout mice, which were infected with ZIKV at 10⁵ PFU (plaque-forming unit) by retro-orbital infusion. ZIKV infection resulted in a marked decrease in claudin-5, occludin, JAM-3, and ZO-1 expression levels in these mice. In addition, ZIKV affected the expression of FIS1 protein levels and the respiratory complexes of II, III, and IV in mice lacking <i>Bmal1</i> expression in endothelial cells.</p> Conclusions <p>Findings from this study contribute to a better understanding of the impact of circadian misalignment on the pathology of ZIKV infection in the adult brain.</p> Graphical abstract <p></p>