Uterine leiomyoma is the most common tumor in women and can cause severe morbidity. Leiomyoma growth requires maintenance and proliferation of a stem cell population. Dysregulated DNA methylation has been reported in leiomyoma, but its role in leiomyoma stem cell regulation remains unclear. Here, we FACS sorted cells from human leiomyoma tissues into three populations: stem-cell like cells (LSC, 5%), intermediate cells (LIC, 7%), and differentiated cells (LDC, 88%) and analyzed the transcriptome and epigenetic landscape of leiomyoma cells at different differentiation stages. LSC harbored a unique methylome, with 8862 differentially methylated regions compared to LIC and 9444 compared to LDC, most of which were hypermethylated. Consistent with global hypermethylation, transcript levels of TET1 and TET3 methylcytosine dioxygenases were lower in LSC. Integrative analyses revealed an inverse relationship between methylation and gene expression changes during LSC differentiation. In LSC, hypermethylation suppressed genes important for myometrium- and leiomyoma-associated functions, including muscle contraction and hormone action, to maintain stemness. The hypomethylating drug, 5'-Aza stimulated LSC differentiation, depleting the stem cell population and inhibiting tumor initiation. Our data suggest that DNA methylation maintains the pool of LSC, which is critical for the regeneration of leiomyoma tumors.