Patients with Chronic Kidney Disease (CKD) have an increased risk and poor prognosis of becoming diagnosed with urothelial carcinoma. Currently, the linking mechanisms underlying the connection between CKD and urothelial carcinoma are not well understood. CKD with declined renal function is associated with the accumulation of circulating indoxyl sulfate, a metabolite synthesized from tryptophan by gut microbes. We investigated the roles of CKD-related uremic toxins in regards to their linking with urothelial carcinoma by delivering indoxyl sulfate to urothelial carcinoma cells and tumor-bearing mice. Upon exposure to indoxyl sulfate, urothelial carcinoma T24 and NTUB1 cells increased proliferation, accompanied by enhanced glutamine uptake and metabolism. Mechanistically, Runt-Related Transcription Factor 2 (Runx2) had been identified as a contributor of both urothelial carcinoma cell proliferation and Solute Carrier Family 1 Member 5 (SLC1A5)-mediated glutamine uptake, while metabolism was demonstrated as being a target to the actions of Runx2 promoted by indoxyl sulfate. An elevated expression of Runx2 caused by indoxyl sulfate correlated with both a reduction of microRNA-204 and an induction of DNA Methyltransferase 1 (DNMT1). MicroRNA-204 agomiR decreased Runx2 expression, while DNMT1 inhibitors reversed indoxyl sulfate-induced reduction of miR-204 and induction of Runx2. Additionally, inhibition of the Aryl Hydrocarbon Receptor (AhR) alleviated indoxyl sulfate-induced signaling changes and cell proliferation. The cancer-promoting effects of indoxyl sulfate were further demonstrated in tumor-bearing mice. In short, our results suggest that indoxyl sulfate may act as a bridge in linking the gap between CKD and urothelial carcinoma by involving the enhancement of glutamine uptake and metabolism.