Background <p>Chordoma is a devastating rare tumor with a poor prognosis, limited therapeutic options and a high recurrence rate. The exploration of novel therapeutic targets has important clinical significance in chordoma diagnosis, treatment, and outcome prediction.</p> Methods <p>In this study, chordoma patients with histopathologically verified disease and KI67 proliferation index data were enrolled. The peripheral eosinophil counts of chordoma patients were summarized, the antitumor effects of eosinophils against chordoma cells were investigated using a coculture experiment, and the potential mechanisms were analyzed.</p> Results <p>The chordoma patients were classified into two groups according to KI67 proliferation index: 1) ≤ 5% (<i>n</i> = 62), and 2) &gt; 5% (<i>n</i> = 80). The results showed that peripheral eosinophil and tumor-infiltrated eosinophil counts decreased with increased KI67 proliferation index, peripheral eosinophil counts deceased after tumor recurrence, and eosinophils could inhibit chordoma cells proliferation by inducing apoptosis and secreting inflammatory cytokines (TNF-α, IL-2 and IFN-γ); moreover, this apoptotic effect could be reversed by blocking TNF-α.</p> Conclusions <p>The current study suggests that eosinophils may be a new target for immunotherapy against chordoma.</p>