The present study aimed to define and validate a protocol to determine the prerequisites, simulation variables and verification parameters that allow evaluate properly the performance of a natural ventilation system in tropical climates, and ensure proper operation for its implementation in a construction project. To do this, it was developed a literature review concerning standards criteria currently established to assess natural ventilation in the most recognized certification systems for sustainable construction, and simulation tools used to model and verify natural ventilation systems, such as thermal simulation, simulation of computational fluid dynamics (CFD) and bulk airflow simulation. Then, it were determined the sought simulation and verification criteria, from a review of reports of natural ventilation design of projects that are applying for sustainable building certifications, and interviews were conducted with key stakeholders of the designs. Hence, it was obtained the required synthesis of evaluation criteria and verification protocols, which was adjusted and approved through discussion and consensus of a panel of experts in the focus group stage. At the same time, a simulation experiment was carried out to understand the relationship between the overall minimum ventilation rates throughout the year and minimum rates recorded by simulating critical conditions for system performance. Finally, a verification protocol was generated and its implementation was revised in three pilot projects that were looking for a sustainable construction certification. It is expected that this product will encourage the use of natural ventilation systems as an efficient solution that minimizes energy use and comply with requirements of indoor air quality.