Objectives Gastric cancer (GC) is a multifactorial disease and the fifth most frequent diagnosed cancer worldwide. It accounts for one third of cancer-related mortalities. Geospatial analysis using geographical information systems (GIS) can provide an efficient solution to identify spatial disparities associated with GC. As such, GIS enables policymakers to control cancer in a better way and identify the regions where interventions are needed. This study aims to publish a comprehensive dataset, which was applied to conduct a spatial analysis of GC patients in the city of Mashhad, Iran. Data description We provide a personal geodatabase, a Microsoft Access database that can store, query, and manage both spatial and non-spatial data, which contains four feature classes. “Male_Stomach_Cancer_Patients” and “Female_Stomach_Cancer_Patients” are point feature classes, which show the age and geographical location of 1156 GC cancer patients diagnosed between 2014 and 2017. “Air_Polution_Mashhad” is another point feature class that reveals the amount of six air pollutants, which was taken from Mashhad Environmental Pollutants Monitoring Center between 2017 and 2018. Finally, “Stomach_Cancer_and_Risk_Factors” is a polygon feature class of neighborhood division of Mashhad, consisting of contributor risk factors including dietary habits, smoking, alcohol use, body mass index and population by age groups for all 165 city neighborhoods.