Insomnia is a major concern among stressed workers worldwide. Although stress generally has a detrimental effect on sleep quality, the impact of biological stress, especially the immunological stress response, on sleep quality is not yet fully understood. Stressed workers were recruited through a screening process using a Brief Job Stress Questionnaire. The participants were asked to complete various occupation-related questionnaires. Additionally, saliva samples were collected to assess interleukin-6 (IL-6) levels as an immunological stress response. Subsequently, they were asked to wear an Apple Watch to record their sleep pattern for one week. Their sleep architecture was estimated using a previously published and validated method. Finally, data from 73 participants were analyzed. Our multivariable analysis revealed that shorter durations of slow-wave sleep (non-rapid eye movement sleep stage 3) were significantly associated with elevated IL-6 levels (p = 0.005) and greater daytime sleepiness (p = 0.002) after controlling for total sleep time. Our finding that a higher immunological stress response is associated with poor sleep quality contributes to a better understanding of insomnia in stressed workers and emphasizes the importance of stress management in this population.