Greater workplace social capital (WSC) can be related to workers’ health and productivity. We sought to clarify the association between horizontal WSC and presenteeism and sickness absence (SA) and to examine the effects of psychological distress on these associations among Japanese workers. A cross-sectional study was conducted in 2017 at seven large Japanese companies. Logistic regression analysis was performed with presenteeism and SA as the dependent variables, horizontal WSC as an independent variable, and sociodemographic characteristics and psychological distress as covariates. After adjustment for sociodemographic characteristics, the results showed that greater horizontal WSC was associated with lower presenteeism and SA. The odds ratios for the relationship between horizontal WSC and presenteeism and that between horizontal WSC and SA dropped moderately after adjustment for psychological distress but remained significant. Further exploration of the factors underlying the relationship between WSC and productivity is needed to confirm if WSC enhances workers’ health and productivity and to inform the development of effective occupational health initiatives.