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Objective Shift work may impact headaches, significantly affecting quality of life and productivity. This study aims to investigate the relationship between shift work and headache occurrence among Dutch female nurses.Material and Methods Participants completed questionnaires in 2011 (N = 59,768) and in 2017 (N = 37,730) reporting on headaches, work history, sleep problems, lifestyle factors, among other factors. Logistic regression analysis was conducted to determine the association between shift work and headache/migraine, as well as the impact of changes in shift work status on headache outcomes.Results Shift work was associated with an increase in headache risk at both baseline (OR = 1.07, 95% CI: 1.02–1.12) and follow-up (OR = 1.07, 95% CI: 0.99–1.15). A similar trend was observed for migraine risk (baseline OR = 1.05, 95% CI: 0.99–1.13; follow-up OR = 1.19, 95% CI: 1.06–1.33). Stratification by shift work duration showed elevated headache risk for those with less than 20 years of shift work, but a reduced risk after 20 years (OR = 0.86, 95% CI: 0.78 – 0.95). Additionally, quitting shift work increased the odds of headache recovery (OR = 1.20, 95% CI: 1.04–1.38).Conclusion The findings show a positive relationship between shift work and headache/migraine risk.