Circadian misalignment, due to shiftwork and/or individual chronotype and/or social jetlag (SJL), quantified as the difference between internal and social timing, may contribute to cardiovascular disease. Markers of endothelial dysfunction and activation of the coagulation system may predict cardiovascular pathology. The present study aim was to investigate the effects of shift work, SJL, and chronotype on endothelial function and coagulation parameters. One hundred female nurses underwent endothelial function testing using the EndoPAT and blood sampling for coagulation markers, repeated at 06:00–9:00 and 18:00–21:00. We found that compared with day workers, endothelial function and fibrinogen levels were lower (p = 0.001, p = 0.005, respectively) and the procoagulant parameters of plasminogen activator inhibitor-1 (PAI-1) and heparanase level and activity were higher amongst shift workers (p = 0.009, p = 0.03, p = 0.029, respectively). High SJL was associated with lower endothelial function (p = 0.002) and higher PAI-1, heparanase procoagulant activity, heparanase level, and D-Dimer level (p = 0.004, p = 0.003, p = 0.021, p = 0.006, respectively). In the late chronotype, PAI-1 and heparanase procoagulant activity were higher than in the early chronotype (p = 0.009, p = 0.007, respectively). Diurnal variation was found for PAI-1, von-Willebrand factor (vWF), heparanase, and heparan-sulfate with higher levels in the mornings. The correlation between shift/day workers and SJL or chronotype was moderately strong, indicating that SJL and chronotype are independent factors. In conclusion, findings suggest endothelial impairment and increased thrombotic risk in nurses working in shifts or with high SJL or late chronotype. The thrombotic risk is increased in the morning independent of circadian misalignment cause. These findings strengthen the importance of the alliance to the biological daily rhythm in daily life. Further research is needed to evaluate inhibitors of heparanase to attenuate the thrombotic risk in individuals with circadian misalignment.