The mucosal surface of the gastrointestinal tract directly interacts with the mucosal lumen, which is continuously exposed to foreign antigens. Specialized intraepithelial lymphocytes (IELs), located between the basolateral surfaces of the epithelial cells, are important as the first line of defense against microbes as well as for their role in the maintenance of epithelial barrier homeostasis. Although IELs are mainly composed of T cells, they are phenotypically and functionally distinct from T cells in peripheral blood or the spleen. Not only are IELs stimulated by the antigens of the intestinal lumen but are they also stimulated by regulatory immune cells. The integrity of the intestinal mucosal barrier is closely tied to the IEL function. Cytokines produced by IELs modulate the cellular functions that trigger the downstream signaling pathways and mediate the barrier homeostasis. In this review, we will address the broad spectrum of cytokines that are derived from IELs and the functional regulation of these cytokines on the intestinal barrier.