The aim of the present study was to investigate the relationship between physical fitness, heart rate variability (HRV) and cognitive function in 37 male sailors from the Royal Norwegian Navy. All subjects participated in an 8-week training program, after which the subjects completed the initial cognitive testing (pretest). The subjects were assigned into a detrained group (DG) and a trained group (TG) based on their application for further duty. The DG withdrew from the training program for 4 weeks after which all subjects then completed the cognitive testing again (post-test). Physical fitness, measured as maximum oxygen consumption (VO2(max)), resting HRV, and cognitive function, measured using a continuous performance task (CPT) and a working memory test (WMT), were recorded during the pre-test and the post-test, and the data presented as the means and standard deviations. The results showed no between-group differences in VO2(max) or HRV at the pre-test. The DG showed a significant decrease in VO2(max) from the pre- to the post-test and a lower resting HRV than the TG on the post-test. Whereas there were no between-group differences on the CPT or WMT at the pre-test, the TG had faster reaction times and more true positive responses on tests of executive function at the post-test compared to the pre-test. The DG showed faster reaction times on non-executive tasks at the post-test compared to the pre-test. The results are discussed within a neurovisceral integration framework linking parasympathetic outflow to the heart to prefrontal neural functions.