Background <p>Physical exercise can cause neuroendocrine activation, which increases salivary cortisol concentrations. Until now there have been no studies comparing the acute effects of endurance and coordinative exercise on cortisol. </p> Objective <p>To examine the effects of an acute bout of endurance vs. coordinative exercise with the same intensity and duration with an intraindividual comparison.</p> Methods <p>61 female and male students between 18 and 30&#xa0;years completed an acute coordinative exercise (Co) and one week later an endurance exercise (En) of the same exercise intensity, which was self-set on the first day, with a heart rate of between 64–76% of maximum over a period of 15&#xa0;min. To measure changes in the hypothalamic–pituitary–adrenal axis activity, saliva samples were collected before (t0 and after exercise (t1: 5&#xa0;min, t2: 30&#xa0;min). </p> Results <p>Baseline values of cortisol (t0) did not differ significantly (t(55) = .233, <i>p</i> = .816). Analysis of variance revealed main effects for type of exercise (<i>F</i> (1) = 5.587, <i>p</i> = .022<i>,</i> η² = .092) and measurement point (<i>F</i> (2) = 22.472, <i>p</i> &lt; <i>.001,</i> η² = .290) as well as an interaction effect of the two factors (<i>F</i> (2, 110) = 4.322, <i>p</i> = .016<i>,</i> η² = .073). Post hoc tests indicated that in the Co group the cortisol t2 values differed significantly from t0 to t1. In the En group, however, t1 differed significantly from t0 to t2. Moreover, cortisol levels differed significantly between Co and En at t2 (t(55) = 3.661, <i>p</i> = .004).</p> Conclusion <p>For the first time we showed that Co produced a higher cortisol release than En of the same exercise intensity and duration. Interventions such as Co require higher cognitive engagement resulting in higher cortisol than En.</p> Trial Registration <p>DRKS, Deutsches Register Klinischer Studien. Registered 20 July 2020, <a href="https://drks.de/search/de/trial/DRKS00016590">https://drks.de/search/de/trial/DRKS00016590</a>.</p>