This study aims to compare the vulnerability analysis between Tenable Nessus Scanner and OWASP Zed Attack Proxy (ZAP) for improving the security of the Human Resource Information System (HRIS) website at Universitas Merdeka Malang. The research methodology includes the use of both Nessus and OWASP ZAP tools to scan the HRIS website for potential vulnerabilities. The findings of this research indicate that OWASP ZAP identified several critical web application vulnerabilities such as the absence of Anti-CSRF tokens, lack of Content Security Policy (CSP) headers, and missing Anti-Clickjacking headers, which are essential for maintaining the security and integrity of user data. On the other hand, Nessus Scanner focused more on network and server infrastructure vulnerabilities. The results suggest that OWASP ZAP is more effective for web application security in this context. Recommendations are provided to address the identified vulnerabilities and enhance the overall security of the HRIS website.