Chordomas are rare but locally aggressive cancer, which originate from primitive notochord remnants. Guidelines have recently been proposed to include the option of choosing chordomas in different locations. However, there is still a great challenge in the modern management of chordomas, primarily due to the high recurrence rate and poor prognosis. On this basis, there is a high demand for new therapeutic approaches and reliable prognostic factors. Recent progress in studying the molecular basis of this specific type of cancer has deepened the understanding of this mechanism, which overall facilitates the discovery of specific biomarkers or indicators of the disease. It also gives rise to potential targeted therapies against chordomas as evidenced by the fact that some RTK inhibitors in a clinical context have been evaluated in relation to chordomas. This article summarizes these achievements including the studies relative to pathogenesis, prognostic factors, and targeted therapies for chordomas. The theme of existing problems is also mentioned, which would facilitate general future efforts in this field.