During the recent decades, social inequalities in mental health have increased and are now one of the most persistent features of contemporary society. There is limited knowledge about when this pattern emerged or whether it has been a historically fixed feature. The objective of this study was to assess whether socioeconomic and gender gaps in mental health changed during the period 1900–1959 in Sweden. We used historical micro data which report all necessary information on individuals’ demographic characteristics, occupational attainment and mental disorders (N = 2,450) in a Swedish population of 193,893. Changes over time was tested using multilevel Cox proportional hazard models. We tested how gender-specific risks of mental disorder changed and how gender-specific socioeconomic status was related to risks of mental disorder later in life. We found a reversal in gender gaps in mental health during the study period. Women had a lower risk than men in 1900 and higher risks in 1959. For men, we found a negative gradient in SES risks in 1900 and a positive gradient in 1959. For women, we found no clear SES gradient in the risk of mental disorder. These findings suggest that the contemporary patterns in socioeconomic and gender gaps in mental disorder emerged during the 1940s and 1950s and have since then persisted.