Natural ventilation in low-budget elementary schools is the main focus to ensure the health and comfort of its occupants, specifically when looking at the global pandemic related to SARS-COV-2. This paper presents an experimental and novel study of natural ventilation in a public elementary school (Los Zumacales), with a particularly low economic budget. The study was carried out during the winter months of the Covid 19 pandemic. The school is located in the rural area of Castilla y León (North-Western Spain) far from high traffic roads. In this study, a methodology of measuring CO2 concentration was applied in nine classrooms in a school. The experimental study shows the level of natural ventilation in each classroom, expressed in Air Changes per Hour (ACH), using the Decay CO2 concentration method. The method is proven by comparing the experimental values of the obtained ACH with those determined by the most powerful methods to achieve appropriate ventilation levels. Thus, ensuring health protection protocol in rural schools, against the COVID 19 pandemic. Harvard guide and Spanish regulations (RITE), two widely recognized methods have been used together with the experimentally obtained standard by Rey et al. Only one classroom showed a value lower than 3 indicating poor ventilation. In this study, the degree of thermal comfort in the nine classrooms were also analyzed according to the EN15251 standard. An average indoor temperature of approximately 19 °C was obtained, and the relative humidity was stable and correct according to Spanish regulations. In addition, the risk of infection in each classroom was estimated following the international method recommended by the federation of European Heating, Ventilation, and Air Conditioning Associations (REHVA). The probability of infection in all the cases studied was less than 14%.