The ubiquitous protein CD46, a regulator of complement activity, promotes T cell activation and differentiation towards a regulatory Tr1-like phenotype. CD46-mediated differentiation pathway is defective in several chronic inflammatory diseases, underlying the importance of CD46 in controlling T cell function and the need to understand its regulatory mechanisms. Using an RNAi-based screening approach in primary T cells, we have identified that two members of the G-protein coupled receptor (GPCR) kinases were involved in regulating CD46 expression at the surface of activated cells. We have investigated the role of prostaglandin E2 (PGE2), which binds to the E-prostanoid family of GPCRs through four subtypes of receptors called EP1-4, in the regulation of CD46 expression and function. Conflicting roles of PGE2 in T cell functions have been reported, and the reasons for these apparent discrepancies are not well understood. We show that addition of PGE2 strongly downregulates CD46 expression in activated T cells. Moreover, PGE2 differentially affects T cell activation, cytokine production and phenotype depending on the activation signals received by the T cells. This was correlated with a distinct pattern of the PGE2 receptors induced, with EP4 being preferentially induced by CD46 activation. Indeed, addition of an EP4 antagonist could reverse the effects observed on cytokine production observed following CD46 costimulation. These data demonstrate a novel role of the PGE2-EP4-GRK axis in CD46 functions, which might at least partly explain the diverse roles of PGE2 in T cell functions.