Abstract Background Access to medical institutions is crucial to healthcare systems. Japan has universal health coverage and unrestricted access to medical institutions; patients can visit any medical institution without requiring referral letters. We developed the Japan- Spatial Accessibility Scale for Medical Institutions (J-AMI) to provide integrated spatial accessibility to multiple sized healthcare institutions. We also examined the association between the J-AMI and life expectancy. Methods This study included 220,621 administrative census mesh blocks defined by address; 89,248 clinics and 8,181 hospitals across 47 provinces in Japan, with a total population of approximately 126 million. The road distance between the centre of each block and the nearest clinic was calculated and scored every 1 km. Hospitals were classified as secondary and tertiary hospitals based on the availability of emergency and critical care centres. Secondary and tertiary hospitals were scored every 2 and 4 km, respectively. The scores for clinics and secondary and tertiary hospitals (1-8 points each) were aggregated and scored using a mesh. The population-weighted municipal J-AMI (PWM-J-AMI) scores were calculated for each municipality. Correlations between the PWM-J-AMI scores and life expectancy by municipality were examined. Geographic information was analysed using ArcGIS Pro. Results Median life expectancies for male and female individuals were 81.4 years (interquartile range [IQR]: 80.9-81.9 years) and 87.5 years (IQR: 87.2-88.0 years), respectively. The median PWM-J-AMI score was 9.5 (IQR: 5.4-14.5). The PWM-J-AMI scores were negatively correlated with male and female individual’s life expectancy by municipality (r=-0.29, p < 0.01 and r = 0.18, p < 0.01, respectively). Conclusions The results suggest that the better a region’s access to medical care, the longer its life expectancy. Efficient medical institution allocation and telemedicine promotion may be essential to improving access. Key messages • We developed the Japan- Spatial Accessibility Scale for Medical Institutions (J-AMI) to provide integrated spatial accessibility to multiple sized healthcare institutions, using ArcGIS Pro. • The PWM-J-AMI scores were negatively correlated with male and female individual’s life expectancy by municipality, which suggest that the better a region’s access, the longer its life expectancy.