Ovarian cancer stem cells (CSCs) drive chemoresistance and tumor relapse through metabolic adaptability and enhanced mitochondrial function. Emerging evidence implicates peroxisome proliferator-activated receptor α (PPARα) as a critical regulator of CSC metabolism. Expression profiling and functional analyses revealed that PPARα expression and PPAR transcriptional activity were markedly elevated in ovarian CSCs. Although the conventional antagonist GW6471 suppressed CSC viability, it failed to fully eradicate the CSC population, indicating the need for a more potent blockade of this axis. To identify a more effective PPARα antagonist, we screened a library of newly synthesized compounds and selected MHY5535 as a lead compound with preferential cytotoxicity toward CSCs. MHY5535 inhibited PPARα transcriptional activity with an IC ₅₀ of 0.54 μM and disrupted mitochondrial energy metabolism in CSCs, significantly reducing the oxygen consumption rate, ATP production, and fatty acid dependency. In silico docking and molecular dynamics simulations demonstrated that MHY5535 achieves stable binding with the PPARα ligand-binding domain through optimized hydrophobic packing. Functionally, MHY5535 exhibited preferential cytotoxicity toward CSCs over non-CSCs (IC ₅₀ : 6.22 μM vs. 10.13 μM) and synergistically enhanced the effects of doxorubicin and cisplatin, as confirmed by combination index analysis. In vivo, combination treatment in a CSC-derived xenograft model resulted in significantly greater tumor growth inhibition compared with monotherapy, without observable systemic toxicity. Taken together, our findings demonstrate that targeting PPARα-driven lipid metabolism sensitizes chemoresistant ovarian CSCs to standard chemotherapy. This approach represents a potential strategy to overcome CSC-mediated drug resistance in advanced ovarian cancer.