Cancer stem cells (CSCs) are indicated to play critical roles in drug resistance, recurrence, and metastasis of cancer. Although molecular targeted therapies have contributed to the improvement of cancer treatments by targeting vulnerable pathways indispensable to the proliferation and survival of cancer cells, no relevant therapeutic modalities targeting CSCs have been developed yet. This review focuses on MELK (maternal embryonic leucine zipper kinase), TOPK (T-lymphokine-activated killer cell-originated protein kinase), and TTK (tyrosine threonine kinase), which are over-expressed frequently in human cancers and play indispensable roles in the development and maintenance of cancer stem cells. In addition, we will discuss recently developed small molecules for these protein targets, which have shown remarkable anti-tumor efficacies in several preclinical studies.