High level of work-family conflict (WFC) is an important risk factor for stress-related health outcomes. However, many studies are cross-sectional studies. In this study, we aimed to clarify how changes in WFC levels over a period 5 yr can affect workers’ mental and physical health, and to clarify whether there are gender differences of them. This study examined 1,808 civil servants (1,258 men and 550 women) aged 20–65 yr working in a local government in the west coast of Japan from 2003 to 2008. Logistic regression analyses were used to examine whether the change in WFC contributes to workers’ health problems and whether there are gender differences. This study revealed association sustained high WFC and deterioration of WFC conflict with poor mental health and poor job satisfaction for both men and women. In men high WFC conflict and deterioration was associated with poor mental health (OR=2.74). On the other hand, women had strong relationship between WFC changes and poor physical health (OR=2.64). WFC was an important factor as a social determinant of health of Japanese civil servants, and the change in WFC affects subsequent health problems with different trends in men and women.