CTCF is a DNA binding protein proposed to act both as a classical transcription factor and as a regulator of chromatin conformation. CTCF is essential in mammals, but the full extent of its involvement in gene regulation is unknown. The canonical Wnt signaling pathway, a vital determinant during development, drives specific gene expression programs. Connections have been made between CTCF and other developmental processes, but its actions in Wnt signaling remain elusive. The aim of this study was to explore whether CTCF binds DNA differentially as a result of Wnt signaling, and how this would affect gene expression. Cleavage Under Targets and Release Using Nuclease technology was used to map the genome-wide binding of CTCF to DNA in HEK293T cells in Wnt ON and OFF conditions. β-catenin and TCF/LEF knockout cell lines were also used to test CTCF’s reliance on these factors. Differentially bound loci were interrogated bioinformatically and correlated with gene expression data. Results revealed novel β-catenin and TCF/LEF dependent CTCF binding sites upon Wnt stimulation. Some loci had no apparent connections to gene regulation, while others correlated with differentially expressed Wnt target genes. Individual instances of Wnt-induced CTCF binding to enhancer regions of target genes suggested that CTCF mediated enhancer-promoter interactions, contributing to differential gene expression. Overall, the results indicate a new role for CTCF in Wnt signaling that warrants further investigation The generation of a CTCF knockout cell line would allow more detailed analysis of the requirement of CTCF for the Wnt signaling response.