Background <p>Biomedical waste (BMW) management in animal research facilities is an emerging challenge due to rising waste volumes, hazardous materials, and the presence of emerging contaminants.</p> Aim <p>This review examines the critical importance of proper onsite segregation of BMW in animal research facilities to safeguard occupational safety, public health, and environmental sustainability.</p> Methods <p>Literature published between 2009 and 2025, including pandemic-era studies, case reports, and regulatory guidelines, was reviewed to identify existing gaps, best practices, and compliance strategies relevant to animal research facilities.</p> Results <p>Improper segregation was found to increase occupational hazards, environmental contamination, and regulatory non-compliance. Key challenges include handling emerging contaminants, pharmaceutical residues, and sharps. Structured training programs, checklist-based audits, and digital monitoring systems were identified as effective strategies for improving segregation accuracy.</p> Conclusion <p>Strengthening staff adherence, infrastructure readiness, and integrating digital monitoring can enhance onsite segregation practices. Future prospects include AI-assisted monitoring tools and adaptive training frameworks to ensure sustainable BMW management in animal research facilities worldwide.</p>