Background We investigated the regional differences in all mental disorder disability pensions (DP) between 2010 and 2015 in Finland, and separately in mood disorders and non-affective psychotic disorder DP. We also studied the contribution of several district-level contextual and mental health service factors to mental disorder DP. Methods Subjects were all those granted mental disorder DP for the first time between 2010 and 2015 in Finland (N = 36,879). Associations between the district-level contextual and mental health service factors and regional DP risks collected from the year 2015 were studied with negative binomial regression analysis in the Finnish hospital districts. The population number on the age (18 to 65 years), gender, occupational status and residential hospital district of the Finnish population from 2015 was used as exposure in the model. Results Significant differences in the regional mental disorder DP risks between and within hospital districts did not appear to follow the traditional Finnish health differences. A lower risk of DP was associated with contextual indicators of higher regional socioeconomic level. Furthermore, population density as a proxy for access to mental health services indicated a higher regional DP risk for lower density in all mental (IRR 1.10; 95% CI 1.06–1.14) and mood disorder (IRR 1.12; 95% CI 1.08–1.16) DP. Both the highest and the lowest regional numbers of all mental health outpatient visits were associated with a higher DP risk in all mental and mood disorder DP, whereas particularly low regional numbers of inpatient treatment periods and of patients were associated with a lower risk of DP. Conclusions In this comprehensive population-level study, we found evidence of significant regional variation in mental disorder DP and related district-level factors. This variation may at least partly relate to differences in regional mental health service systems and treatment practices. Adapting to the needs of the local population appears to be indicated for both regional mental health service systems and treatment practices to achieve optimal performance.