The dysregulation of histone deacetylases (HDACs) is closely associated with tumorigenesis and has emerged as a promising target for anti-cancer drugs. Some odd-chain fatty acids are present in trace levels in human tissue. Despite limited health benefits, there is increasing experimental evidence of nutritional benefits of odd-chain fatty acids. This study examines the effects of five odd-chain fatty acids (valeric, heptanoic, nonanoic, undecanoic, and pentadecanoic acid) as novel HDAC6 inhibitors. Examination of these fatty acids on the proliferation and clonogenic ability in various cancer cell lines revealed that pentadecanoic and undecanoic acid can strongly inhibit cancer cell proliferation. Heptanoic and nonanoic acid showed moderate anti-proliferative effects, while valeric acid demonstrated weak anti-proliferative effects. HDAC6 inhibitory activities were in the order of pentadecanoic acid (C15:0) > undecanoic acid (C11:0) > nonanoic acid (C9:0) > heptanoic acid (C7:0) > valeric acid (C5:0), consistent with the anti-proliferative assay results. All of these fatty acids promoted the acetylation of α-tubulin in MCF-7 breast and A549 lung cancer cells dose-dependently. In-silico molecular docking analysis showed that increasing the aliphatic carbon chain length facilitates binding to HDAC6 residues, which might be important for the inhibitory potential of HDAC6. This study shows the potential utility of odd-chain fatty acids for epigenetic-based cancer therapy.