Background: Anaplastic thyroid carcinoma (ATC) is still one of the most aggressive and refractory cancers, and a therapy with a new concept needs to be developed. Recently, the research of cancer stem cells (CSCs) has been progressed, and CSCs have been suggested to be responsible for metastasis, recurrence, and therapy resistance. In ATC-CSCs, aldehyde dehydrogenase (ALDH) activity is the most reliable marker to enrich the CSCs; however, it itself is just a marker and is not involved in CSC properties. In the present study, therefore, we aimed to identify key signaling pathways specific for ATC-CSCs. Methods: The siRNA library targeting 719 kinases was used in sphere formation assay and cell survival assay using ATC cell lines to select target molecules specific for the CSC properties. The functions of the selected candidates were confirmed by sphere formation, cell survival, soft-agar, and nude mice xenograft assays using small compound inhibitors. Results: We focused on PDGFR, JAK, and PIM, whose siRNAs had the higher inhibitory effect on sphere formation and also lower/no effect on regular cell growth in both FRO and KTC3 cells. Next, we used inhibitors of PDGFR, JAK, STAT3, PIM and NF-κB, and all of them successfully suppressed sphere formation in a dose-dependent manner but not regular cell growth, conforming the screening results. Inhibition of the JAK/STAT3 and NF-κB pathways also reduced anchorage-independent growth in soft agar and tumor growth in nude mice. Conclusions: These results suggest that JAK/STAT3 and NF-κB signals play important roles in ATC-CSCs. Targeting these signaling pathways may be a promising approach to treat ATC.