Internationalization and technological developments have changed the work organization in developed and developing industrial economies. Information and communication technologies, such as computers and smartphones, are increasingly used, allowing more temporal and spatial flexibility of work. This may lead to an increase in supplemental work, i.e. constant availability or working in addition to contractually agreed work hours. This in turn extends work hours and leads to work hours in evenings and weekends, causing interferences of work hours with biological and social rhythms for sleep, recovery and social interaction. However, empirical findings on the effects of supplemental work and work hours on occupational health are rather scarce. Therefore, the aim of this study was to investigate the association between (1) work-related contacts outside of regular work hours and (2) working in the free time with self-reported work-related health impairments in the fourth and fifth European Working Conditions Surveys (EWCS 2005, EWCS 2010). Out of these cross-sectional, large-scale surveys, data on n = 22 836 and n = 34 399 employed workers were used for weighted logistic regression analyses. About half of the sample reported at least occasional supplemental work. The results showed an increased risk of reporting at least one health problem for employees who had been contacted by their employer (EWCS 2005), or worked in their free time to meet work demands (EWCS 2010) in the last 12 months, compared to those reporting no supplemental work or work-related contacts during free time. These results were controlled for demographic variables, physical and mental work load, worker autonomy, and several work hours characteristics (e.g. hours per week, unusual and variable hours). The risk of reporting health problems was increased by being contacted both sometimes (Odds Ratio [OR] 1.26, 95% Confidence Interval [CI] 1.14–1.39) and often (OR 1.13, 95% CI 1.02–1.25), whereas the frequency of working in the free time showed a clear dose-response effect (sometimes: OR 1.14, 95% CI 1.04–1.24; often: OR 1.60, 95% CI 1.47–1.75), both compared to the category “never”. The findings, thus, indicate that even a small amount of supplemental work beyond contractually agreed work hours may increase the risk of work-related health impairments. Working in the free time was associated with a substantial risk increase and might be a better indicator for actual work load than being contacted by the employer outside of contractually agreed work hours. Thus, in order to minimize negative health effects, availability requirements for employees outside their regular work hours should be minimized. While these effects definitely need further study, especially regarding a quantification of actual supplemental work and its temporal location, addressing the company culture and using incentives and policies might be options to reduce the amount of supplemental work and maintain the risks of health impairments in the working population at a lower level.