Background: Traffic accidents involving professional drivers have serious societal repercussions. Unique occupational stressors and health risks exacerbate the likelihood of traffic accidents among professional drivers. This study explores the association between presenteeism—impaired work performance due to working while unwell—and traffic accident risk among professional taxi drivers in Japan. Methods: A prospective cohort study was conducted from June 2022 to February 2023, involving taxi drivers from a single company in Fukuoka Prefecture, Japan. Presenteeism was assessed using the Work Functioning Impairment Scale (WFun). Primary outcome involved the number of self-reported minor traffic accidents. The incidence rate ratio (IRR) of minor traffic accident occurrences was estimated using a Poisson regression analysis, adjusted for confounders including sex, age, and driving experience. Results: Of 838 targeted drivers, 435 were included in the analysis. Higher baseline work functioning impairment was associated with a significant trend of increasing IRR of minor traffic accidents (p for trend = 0.045). A dose-response relationship was seen between the degree of presenteeism and incidence rate of minor traffic accidents. Conclusion Higher levels of presenteeism were associated with an increased risk of traffic accidents among taxi drivers. The findings underscore the need for socio-economic support and prioritized health management to mitigate traffic accident risk among professional drivers. This study highlights the importance of managing non-critical health issues alongside serious health conditions for safer driving practices among professional drivers in Japan.