Background: This study examined the relationship between workplace mistreatment, including discrimination, abuse, and overworking, and health problems among full-time workers prior to and during the coronavirus disease (COVID-19) outbreak in South Korea. Methods: We analyzed data from the 2017 and 2020–2021 Korean Working Conditions Surveys, including the final sample of 44,425 participants. Multiple logistic regression was used to examine the relationship between workplace mistreatment and health problems among workers by gender. Interaction analysis was conducted to establish the association between the COVID-19 pandemic and health problems related to mistreatment. The occupational, demographic, and socioeconomic backgrounds were adjusted. Results: We found a significant association between workplace mistreatment and health problems, including headaches, eyestrain, and anxiety. The association increased after the COVID-19 pandemic: “discrimination” (men (OR 2.26, 95% CI 1.93–2.65), women (OR 2.73, 95% CI 2.36–3.17)); abuse (men (OR 5.42, 95% CI 2.87–10.23), women (OR 4.70, 95% CI 3.12–7.08)); and overworking: men (OR 2.36, 95% CI 2.01–2.77), women (OR 3.52, 95% CI 2.68–4.61). The interaction indicates an increased incidence of people having health problems due to workplace mistreatment (OR 1.03, 95% CI 1.00–1.06) during the COVID-19 pandemic. Conclusion: Statistically, employees who experience workplace mistreatment have worse health conditions. The COVID-19 pandemic has affected the job environment and increased the association between workplace mistreatment and health problems. To eliminate the health problems related to workplace mistreatment, it is necessary to address the impact of the COVID-19 pandemic on work and employee health conditions.