In hospitals, health care workers (HCWs) are exposed to a wide range of respiratory hazards, which requires using respiratory protective equipment and implementing Respiratory Protection Programs (RPPs). The aim of this cross-sectional study was to investigate RPP implementation in 36 teaching hospitals located in the Fars province of Iran. A researcher-developed checklist, including nine components of the RPP standard, was completed by industrial hygienists in the study hospitals. The Fuzzy Analytical Hierarchy Process (FAHP) was used to determine the weight coefficient of RPP components. Finally, a Respiratory Protection Program Index (RPPI) was developed to calculate hospital compliance with RPP. The results showed that RPP were not fully implemented in the studied hospitals, and the highest and lowest RPPI scores were related to training and fit testing, respectively. To promote the implementation of RPP, significant efforts are required for all components, especially fit testing and worker evaluation.