Background Studies in the health care sector indicate that good work time control is associated with better perceived wellbeing but also with non-ergonomic work schedules, such as compressed work schedules. Participatory working time scheduling is a collaborative approach to scheduling shift work. Currently, there is a lack of information on whether working hour characteristics and employees’ wellbeing in irregular shift work change after implementing participatory working time scheduling. Objective To investigate the effects of using digital participatory working time scheduling software on working hour characteristics and well-being among Finnish hospital employees. Participants and methods We compared changes in objective working hour characteristics and wellbeing between 2015 and 2017 among employees (n= 677, mainly nurses and practical nurses) when using participatory working time scheduling software (participatory scheduling, n= 283) and traditional shift scheduling (traditional scheduling, n= 394). The statistical analyses were conducted using the repeated measures general linear model and the generalized logit model for binomial and multinomial variables adjusted for age, sex, education, shift work experience, control over scheduling of shifts at baseline (where applicable) and hospital district. Results The proportion of long work shifts (≥12h) increased to a greater extent (F= 4.642, p= 0.032) with the participatory scheduling than with the traditional scheduling. In comparison to traditional scheduling, the perceived control over scheduling of shifts increased significantly with participatory scheduling (OR 3.24, 95% CI 1.73–6.06). None of the other wellbeing variables showed statistically significant changes in the adjusted models. Conclusions The proportion of long work shifts and perceived control over scheduling of shifts increased more among employees using participatory working time scheduling than among those using traditional scheduling. Otherwise, using participatory working time scheduling software had little effect on both objectively measured working hour characteristics and perceived wellbeing in comparison to traditional scheduling. The results merit confirmation in a larger sample with a longer follow-up.