Heat acclimation is a physiologically and biochemically adapted process when species transition from one environmental temperature to one of the increased temperature. There is very limited epidemiological evidence on the heat-related impacts during exposure to extremely high heat in an occupational environment. This study sought to identify a potential biomarker of heat acclimation and the burden of heat on the body. The aim of this study was to elucidate oxidative DNA damage and heat acclimation through a self-comparison study design in navy boiler tenders, subjects exposed to extremely high heat in an occupational setting. Fifty-eight male soldiers who work in a boiler room were recruited for this study. The subjects were initially assessed with a health examination and body composition assessment before sailing. In order to compare the within-subject differences before and after heat exposure, the index-related heat exposure was collected before and after a routine 5-h work shift and 7-day sailing. Urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG), a useful marker of oxidative DNA damage was the measurement by liquid chromatography/tandem mass spectrometry. The median of the change in urinary 8-OHdG was 0.78 μg/g creatinine, as the urinary 8-OHdG after sailing was significantly higher than before sailing (p < 0.01). The urinary 8-OHdG was significantly decreased in heat-acclimated boiler tenders. Oxidative DNA damage was significantly decreased in heat-acclimated subjects. Urinary 8-OHdG can be used as a biomarker to assess the effect of heat stress as a result of occupational exposure to extremely high heat conditions.