Increased permeability of endothelial cells lining the blood vessels in the brain leads to vascular oedema and, potentially, to stroke. The tight junctions (TJs), primarily responsible for the regulation of vascular permeability, are multi-protein complexes comprising the claudin family of proteins and occludin. Several studies have reported that downregulation of the claudin domain containing 1 (CLDND1) gene enhances vascular permeability, which consequently increases the risk of stroke. However, the transcriptional regulation of CLDND1 has not been studied extensively. Therefore, this study aimed to identify the transcription factors (TFs) regulating CLDND1 expression. A luciferase reporter assay identified a silencer within the first intron of CLDND1, which was identified as a potential binding site of the myeloid zinc finger 1 (MZF1) through in silico and TFBIND software analyses, and confirmed through a reporter assay using the MZF1 expression vector and chromatin immunoprecipitation (ChIP) assays. Moreover, the transient overexpression of MZF1 significantly increased the mRNA and protein expression levels of CLDND1, conversely, which were suppressed through the siRNA-mediated MZF1 knockdown. Furthermore, the permeability of FITC-dextran was observed to be increased on MZF1 knockdown as compared to that of the siGFP control. Our data revealed the underlying mechanism of the transcriptional regulation of CLDND1 by the MZF1. The findings suggest a potential role of MZF1 in TJ formation, which could be studied further and applied to prevent cerebral haemorrhage.