Background: One of the most important risk factors for non-communicable diseases is physical inactivity. This study was conducted to determine the geographical distribution of physical inactivity in Yazd City to identify places that need intervention. Methods: This is a cross-sectional descriptive analysis conducted based on Geographic Information System (GIS). The data for residents between 20 to 69 years in Yazd city of Yazd Health Study (YaHS) yielded 8727 people. The short form of the International Physical Activity Questionnaire (IPAQ-SF) was used. The SPSS V.19 and ARC Map10.5 software were used to analyze the data. Results: The pattern of geographical distribution of physical inactivity in the subgroups of sex, age, and socio-economic status were similar. Spatial auto-correlation analysis showed that physical activity score had a cluster significant level. Also, hot spot analysis showed that this clustering is different in men and women. Using interpolation, the lowest score of physical activity for the central parts of Yazd city and from east to west was estimated. Conclusion: It is necessary to design and implement interventions to promote physical activity for women, older people and those with a better socio-economic status. In the meantime, it is necessary to prioritize areas with lower physical activity, especially in the central part and in the direction from east to west.