Bisphenol A (BPA) is an industrial contaminant and is reported to be a risk factor associated with the development of tumors. In our previous studies, we have shown that BPA promoted the growth of SK-N-SH human neuroblastoma cells and increased their invasion and metastasis. In this study, we further investigated the effects of BPA and 17β-estradiol (E2) on the stem cell-like cells from SK-N-SH cells. Detection of stem cell markers, proliferation assay, and clonogenic analysis showed that the side-population (SP) of SK-N-SH cells had properties similar to those of stem cells. BPA or E2 exposure decreased the percentage of SP cells and the expression of stem cell-marker proteins. BPA and E2 promoted the growth of non-SP cells to a greater extent than of SP cells; in addition, they significantly increased the growth of SP cells. Thus, BPA has effects on stem cell-like cells, which induce tumor formation, and thus, BPA is an environmental factor that plays an important role in the development of neuroblastoma.