We have shown previously that the function of Ycf1p, yeast ortholog of multidrug resistance-associated protein 1 (MRP1), is regulated by yeast casein kinase 2␣ (Cka1p) via phosphorylation at Ser251. In this study, we explored whether casein kinase 2␣ (CK2␣), the human homolog of Cka1p, regulates MRP1 by phosphorylation at the semiconserved site Thr249. Knockdown of CK2␣ in MCF7-derived cells expressing MRP1 [MRP1 CK2␣(Ϫ)] resulted in increased doxorubicin sensitivity. MRP1-dependent transport of leukotriene C 4 and estradiol-17-D-glucuronide into vesicles derived from MRP1 CK2␣(Ϫ) cells was decreased compared with MRP1 vesicles. Moreover, mutation of Thr249 to alanine (MRP1-T249A) also resulted in decreased MRP1-dependent transport, whereas a phosphomimicking mutation (MRP1-T249E) led to dramatic increase in MRP1-dependent transport. Studies in tissue culture confirmed these findings, showing increased intracellular doxorubicin accumulation in MRP1 CK2␣(Ϫ) and MRP1-T249A cells compared with MRP1 cells. Inhibition of CK2 kinase by 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole resulted in increased doxorubicin accumulation in MRP1 cells, but not in MRP1 CK2␣(Ϫ), MRP1-T249A, or MRP1-T249E cells, suggesting that CK2␣ regulates MRP1 function via phosphorylation of Thr249. Indeed, CK2␣ and MRP1 interact physically, and recombinant CK2 phosphorylates MRP1-derived peptide in vitro in a Thr249-dependent manner, whereas knockdown of CK2␣ results in decreased phosphorylation at MRP1-Thr249. The role of CK2 in regulating MRP1 was confirmed in other cancer cell lines where CK2 inhibition decreased MRP1-mediated efflux of doxorubicin and increased doxorubicin cytotoxicity. This study supports a model in which CK2␣ potentiates MRP1 function via direct phosphorylation of Thr249.