Centaurea paphlagonica (Bornm.) Wagenitz is an endemic plant in Turkey. Pyrocatechol, vanillic acid, 3,4‐dihydroxy benzoic acid, 5‐O‐caffeoylshikimic acid, tamarixetin, chlorogenic acid methyl ester, quercetin, 1,3‐dicaffeoylquinic acid, tamarixetin‐7‐O‐β‐D‐glucopyranoside, quercimetrin, daucosterin, paphlagonicanin B, tamarixetin‐7‐O‐β‐rutinoside, rutin, chlorogenic acid, isoorientin, orientin, 3‐O‐feruloylquinic acid, quercetagetin‐3‐methyl ether 6‐O‐β‐glucopyranoside, diosmetin 6‐C‐β‐glucopyranoside, quercetagetin 4′‐methyl ether 7‐O‐β‐glucopyranoside, paphlagonicanin A, nepetin, cirsiliol, desacylcynaropicrin, and 8α‐O‐(2′,3′‐dihydroxyisobutyryl) desacylcynaropicrin were isolated from both flower and aerial parts of C. paphlagonica. These compounds were identified using 1D and 2D NMR methods and ESI‐MS. The MTT assay assessed the antiproliferative activities of all isolated (known and new compounds) compounds on Caco‐2, LNCaP, A549, HeLa, and HEK‐293 cell lines. The 8α‐O‐(2′,3′‐dihydroxyisobutyryl) desacylcynaropicrin demonstrated the highest activity against CaCo‐2 and HeLa cancer cell lines.