CTCF mediated chromatin interactions influence organization and function of mammalian genome in diverse ways. We analyzed the interactions amongst CTCF binding sites (CBS) at murine TCRb locus to discern the role of CTCF mediated interactions in regulation of transcription and VDJ recombination. 3C analysis revealed thymocyte specific long-range intrachromosomal interactions amongst various CBS across the locus that were relevant for defining the limit of enhancer Eb regulated Recombination Centre (RC) and for facilitating the spatial proximity of Trbv segments to RC. Ectopic CTCF binding in the RC region, effected via genetic manipulation, altered CBS directed chromatin loops, interfered with RC establishment and reduced the spatial proximity of RC with Trbv segments. Changes in chromatin loop organization by ectopic CTCF binding were relatively modest but influenced transcription and VDJ recombination dramatically. Besides revealing the importance of CTCF mediated chromatin organization for TCRb regulation, the observed chromatin loops were consistent with the emerging idea that CBS orientations influence chromatin loop organization and underscored the importance of CBS orientations for defining chromatin architecture that supports VDJ recombination. Further, our study suggests that in addition to mediating long-range chromatin interactions, CTCF influences intricate configuration of chromatin loops that govern functional interactions between elements.