Overactive bladder (OAB), which is characterized by the sudden and uncomfortable need to urinate with or without urinary leakage, is a challenging urological condition. The insufficient efficacy of current pharmacotherapies that uses antimuscarinic agents has increased the demand for novel long-term/stable therapeutic strategies. Here, we report the superior therapeutic efficacy of using mesenchymal stem cells (MSCs) for the treatment of OAB and a novel therapeutic mechanism that activates endogenous Oct4(+) primitive stem cells. We induced OAB using bladder-outlet-obstruction (BOO) in a rat model and either administered a single transplantation of human adipose-derived MSCs or daily intravenous injections of solifenacin, an antimuscarinic agent, for 2 weeks. Within 2 weeks, both the MSC- and solifenacin-treated groups similarly demonstrated relief from BOO-induced detrusor overactivity, hypertrophic smooth muscle, and neurological injuries. In contrast with the solifenacin-treated groups, a single transplantation of MSCs improved most OAB parameters to normal levels within 4 weeks. Although the transplanted human MSCs were hardly engrafted into the damaged bladders, the bladder tissues transplanted with MSCs increased rat sequence-specific transcription of Oct4, Sox2, and Stella, which are surrogate markers for primitive pluripotent stem cells. In addition, MSCs enhanced the expression of several genes, responsible for stem cell trafficking, including SDF-1/CXCR4, HGF/cMet, PDGF/PDGFR, and VEGF/VEGFR signaling axis. These changes in gene expression were not observed in the solifenacin-treated group. Therefore, we suggest the novel mechanisms for the paracrine effect of MSCs as unleashing/mobilizing primitive endogenous stem cells, which could not only explain the long-term/stable therapeutic efficacy of MSCs, but also provide promising new therapies for the treatment of OAB.