Remodeling of chromatin structure plays a key role in transcriptional regulation. Lineage-specific changes in chromatin accessibility are well-described but less is known about chromatin remodeling in response to cell perturbation. Because immune cells undergo major changes in gene expression upon activation, we carried out an integrative analysis of chromatin accessibility, 3D genome interactions and whole transcriptome expression in response to activation of primary human CD4+ and CD8+ T cells. Activated T cells exhibited a marked reorganization of chromatin structure. At a lower level, activation was associated with extensive changes in chromatin accessibility that were enriched for regulatory elements. At a higher level, activation was associated with the acquisition of new topologically-associated domain (TAD) boundaries and partitioning of TADs, that were linked to transcriptional changes at specific loci. These findings provide a framework for understanding how activation-associated changes in chromatin architecture relate to gene expression in human T cells.