Objective This study aimed to investigate trends in educational inequalities in poor health and emotional exhaustion during the pandemic among workers, and differences in trends between men and women. Methods Five waves (2019–2021) from the longitudinal study ‘the Netherlands Working Conditions Survey COVID-19 study’ were used (response rates: 32–38%). Generalized logistic mixed models were used to estimate the changes in absolute and relative educational inequalities in poor health and emotional exhaustion for all workers (n = 12,479) and for men and women, separately. Results Low and intermediate educated workers reported more often poor health (OR 2.54; 95% CI 1.71–3.77 and OR 2.09; 95% CI 1.68–2.61, respectively) than high educated workers. Intermediate educated women (OR 0.49; 95% CI 0.37–0.64) reported less emotional exhaustion than high educated women, but no differences were observed among men. The prevalence of poor health first decreased across all educational levels until March 2021, and bounced back in November 2021. A similar pattern was found for emotional exhaustion, but for low and intermediate educated workers only. Relative educational inequalities in poor health reduced among men during the pandemic, and absolute differences decreased among men and women by 2.4–2.6%. Relative educational inequalities in emotional exhaustion widened among men only. Absolute differences in emotional exhaustion first increased among both men and women, but narrowed between the last two waves. Discussion Socioeconomic inequalities for poor self-rated health remained but narrowed in relative and absolute terms during the pandemic. With regard to emotional exhaustion, socioeconomic inequalities returned to pre-COVID-19 levels at the end of 2021.