Background/Objectives: The Centaurea genus is characterized by many species, a broad biological diversity, and a rich secondary metabolite content. These species exhibit various biological activities, including antioxidant, anti-inflammatory, antimicrobial, antiproliferative, and wound-healing properties. However, there are limited anticancer research studies available on the species. This study aims to investigate the potential cytotoxic effects of dichloromethane (CRD) and methanol (CRM) extracts obtained from the root of the endemic Centaurea lycaonica to clarify the mechanism of apoptosis by the intrinsic pathway on the human endometrial cancer cell line RL95-2 based on phytochemical analysis. Methods: The cytotoxicity studies were performed using a Real-Time Cell Analyzer (xCELLigence) and the MTT assay. The activities of caspase 3, caspase 9, Bax, and Bcl-2 were evaluated to investigate the molecular mechanism of apoptosis. LC-HRMS determined the phytochemical content of extracts. Results: CRD and CRM had a concentration-dependent effect in increasing caspase 3 and 9 activities and Bax/Bcl-2 ratios compared to the control with low IC50 values. Conclusions: Apoptosis induction was more pronounced with CRM, which was enriched in hesperidin; this association warrants targeted validation with purified standards.