Six new naphthoquinones, euchronin A–F (1–6) and nine known naphthoquinones (7–15), were isolated from the roots of Arnebia euchroma (Royle) Johnst. The structures of the new compounds were confirmed by extensive spectroscopic analyses, including UV, IR, HR-ESI–MS, 1D and 2D NMR. In the present study, we estimated the anti-proliferative activities of these compounds with HaCaT cells. The results indicated that compounds 2 and 4 showed strong anti-proliferative activities at 25 μM, with relative viability at 38.83% and 68.44%, respectively.Graphical Abstract: