Health care professionals often face irregular working hours and high work pace. We studied associations of the five working time dimensions duration (weekly working hours), timing (shift work and weekend work), on-call work, working time autonomy, and work tempo (deadline and performance pressure) with well-being among health care employees in Finland and Germany. We used data on working time dimensions and indicators of well-being (work-life conflict, poor perceived health, sleep difficulties, and fatigue) from a cohort of 5050 hospital employees (Working Hours in the Finnish Public Sector Study 2015, WHFPS) and 1450 employees in the health care sector in Germany responding to the German BAuA-Working Time Survey in 2015 (BAuA-WTS). Findings from logistic regression analyses showed that high work tempo was associated with increased work-life conflict (WHFPS: odds ratio [OR] = 3.64, 95%CI 3.04–4.36 and BAuA-WTS: OR = 2.29, 95%CI 1.60–3.27), sleep difficulties (OR = 1.75, 95%CI 1.43–2.15 and OR = 1.33, 95%CI 1.03–1.71) and fatigue (OR = 2.13, 95%CI 1.77–2.57 and OR = 1.64, 95%CI 1.29–2.10) in both datasets. Weekend work was associated with increased work-life conflict (OR = 1.48, 95%CI 1.27–1.72 and OR = 1.61, 95%CI 1.12–2.32); and high working time autonomy with decreased work-life conflict (control over the timing of breaks: OR = 0.65, 95%CI 0.55–0.78 and OR = 0.52, 95%CI 0.33–0.81). The associations between other working time dimensions and well-being were less consistent. These results suggest that tight deadlines, performance pressure, weekend work and lack of working time autonomy are linked to impaired well-being among health care employees.