Management of advanced chordomas remains delicate considering their insensitivity to chemotherapy. Homozygous deletion of the regulatory gene has been described as the most frequent genetic alteration in chordomas and may be considered as a potential theranostic marker. Here, we evaluated the tumor efficacy of the CDK4/6 inhibitor palbociclib, as well as the PLK1 inhibitor volasertib, in three chordoma patient-derived xenograft (PDX) models to validate and identify novel therapeutic approaches. From our chordoma xenograft panel, we selected three models, two of them harboring a homozygous deletion of genes, and the last one a pathogenic variant (as control). For each model, we tested the palbociclib and volasertib drugs with pharmacodynamic studies together with RT-PCR and RNAseq analyses. For palbociclib, we observed a significant tumor response for one of two models harboring the deletion of (p = 0.02), and no significant tumor response in the -mutated PDX; for volasertib, we did not observe any response in the three tested models. RT-PCR and RNAseq analyses showed a correlation between cell cycle markers and responses to palbociclib; finally, RNAseq analyses showed a natural enrichment of the oxidative phosphorylation genes (OxPhos) in the palbociclib-resistant PDX (p = 0.02). CDK4/6 inhibition appears as a promising strategy to manage advanced chordomas harboring a loss of . However, further preclinical studies are strongly requested to confirm it and to understand acquired or resistance to palbociclib, in the peculiar view of a targeting of the oxidative phosphorylation genes.