Introduction: The International Health Regulations 2005 require countries to establish laboratory systems for rapid and safe confirmation of public health emergencies including zoonoses. Objectives: This study assessed the national veterinary laboratory system capacity for the confirmation of infectious threats to global health security in Benin. Method: The study was descriptive, cross-sectional and evaluative. The non-probability sampling method with selection of the two existing veterinary laboratories were used. Two questionnaires, one observation grid and the Food and Agriculture Organization laboratory mapping tool-core were used. The system capacity was rated good if each laboratory met at least 80% of the assessed criteria. Otherwise, the capacity was rated insufficient. Results: The national veterinary laboratory system capacity in Benin was insufficient. Bohicon laboratory satisfied 27.2% of assessed criteria; With the laboratory mapping tool-core, Parakou laboratory had an average indicator of 50.7%. Laboratory collaboration and networking was the best performing domain with 66.7%. Only basic supplies category reached 80%. Laboratory budget, sample accession and availaible technology had the lowest scores. The veterinary laboratory system is facing shortage of staffs. Avian influenza virus is confirmed by the two laboratories; Bacillus anthracis and rift valley fever virus are only confirmed by Parakou laboratory. Ebola and Lassa fever are not confirmed. There is no collaboration between the laboratories in the country. Conclusion: The veterinary laboratories are not able to ensure timely detection of zoonoses and inform health system for preparedness. The development and implementation of the veterinary laboratory system improvement plan is essential for the global health security in Benin.