Background: People in lower socioeconomic positions report worse health-related functioning. Only few examined whether perceptions of unfairness are particularly common in these people and whether this perceived unfairness relates to their subsequent poor health outcomes. We thus set out to examine the contribution of perceived unfairness to the higher risks of physical and mental dysfunction in men and women with a lower socioeconomic position. Methods: Seven-year prospective cohort data from the Dutch SMILE study among 1,282 persons, 55 years old and older, were used. Physical and mental health-related functioning was measured with the SF-36, socioeconomic status with income and education, and the perception of unfairness with an extended new measure asking for such perceptions in both work and non-work domains. Results: Perceived unfairness was more common in lower socioeconomic positions. Such perpection was related to both physical (odds ratio = 1.57 (95% confidence interval: 1.17-2.11)) and mental (1.47 (1.07-2.03)) decline, while low socioeconomic position was only related to mental decline (1.33 (1.06-1.67)). When socioeconomic position and perceived unfairness were simultaneously controlled, odds ratios for both determinants decreased only very little. Socioeconomic position and perceived unfairness were for the largest part independently related to longitudinal health-related decline. Conclusions: The general perception of unfairness, at work and beyond work, might have implications for functional decline in middle and older age. We recommend that - rather than addressing and changing individual perceptions of unfairness - more research is needed to find out whether specific environments can be defined as unfair and whether such environments can be effectively tackled in an attempt to truly improve public health.