OBJECTIVES: Research suggests that misalignment of the biological clock and social time, referred to as social jetlag (SJL),can induce physical and mental disorders. SJL may also be associated with presenteeism (i.e., a state in which workers are unable to perform sufficiently due to mental and physical health problems, even though they are going to work). However, the association between SJL and presenteeism among workers in Japan remains unclear. This study aimed to verify the following hypotheses in a sample of workers in an industrial setting in Japan: "Workers exhibiting SJL have a high degree of work functioning impairment due to presenteeism" and "An association between SJL and presenteeism exists, even when taking work style and sleep-related factor into consideration." METHODS: A self-administered questionnaire survey was conducted with 1,573 workers in the manufacturing industry. Of these, 1,501 participants responded (response rate: 95.4%). Individuals who provided invalid answers or used alarm clocks to wake on work-free days were excluded, according to the Munich Chronotype Questionnaire (MCTQ) guidelines. The final sample comprised 980 participants (80.7% male; average age: 44.4 [SD 11.3] years). SJL was assessed using the MCTQ. Presenteeism was measured using the work functioning impairment scale. Using presenteeism as the dependent variable, we conducted hierarchical multiple regression analyses to compare the explanatory power of the different models. Independent variables were SJL, daily rest period between workdays, weekday sleep duration, and subjective insomnia. Models 2 and 3 were adjusted for age, sex, employment position, occupation, employment status, and working regulations. RESULTS: Multiple regression analyses indicated that SJL was significantly and individually associated with presenteeism (β = .066, p = .038). After adjusting for work- and sleep-related variables (Models 2 and 3), SJL no longer contributed significantly to presenteeism. In the final model, daily rest periods (β = .076, p = .017) and subjective insomnia (β = .470, p < .001) remained significantly associated with presenteeism (adjusted R2 = .239). CONCLUSIONS: The hypothesis "Workers experiencing SJL have a high degree of work functioning impairment due to presenteeism" was supported in our univariate analysis. However, after considering the influence of subjective insomnia and daily rest periods, the association disappeared. Therefore, a direct relationship between SJL and presenteeism is not supported. Thus, the risk of presenteeism should be considered in two stages, first confirming the perception of insomnia among workers who experience SJL, and then considering the possibility of presenteeism occurring.