Background: Brachyury has recently garnered attention as both a biomarker and a causative factor in chordoma development, making it a promising therapeutic target. Objectives: Herein, we report a systematic review and meta-analysis to evaluate brachyury as a diagnostic biomarker and therapeutic molecular target in chordomas. Methods: Scopus, PubMed/Medline, Cochrane Library databases, and Web of Science were searched up to July 18, 2024, without any restrictions. The Comprehensive Meta-Analysis version 3.0 software was used to calculate the event rate (ER) with a 95% confidence interval (CI). We utilized STRING to explore functional interactions among the studied genes. Results: Twenty-five studies related to the expression of brachyury and five related to the treatment vaccine of brachyury were included in this category. The ER of brachyury expression among chordoma patients was 92.2% (95% CI: 87.3% - 95.3%), with I² = 74.65%. Among the five studies related to treatment vaccines, there were three studies with Phase 1, one with Phase 2, and a case report. Conclusions: The high expression suggests that brachyury serves as a reliable diagnostic marker for chordomas. The findings indicate potential therapeutic implications for targeting brachyury in chordoma treatment.