Background The phenomenon of exercise‐induced hypoalgesia and concomitant mood changes is well‐established. How exercise‐induced hypoalgesia and affective responses are shaped by the intensity of an acute exercise bout and individual fitness levels is as yet not well‐understood. This study investigates whether heat pain threshold (PTh), pain tolerance (PTol) and affective parameters are modulated by the intensity of an acute exercise bout and/or individuals’ fitness level. Stronger analgesic responses are hypothesized after high‐intensity exercise in physically fitter subjects, possibly in sync with concomitant mood changes. Methods Thirty‐three healthy men were recruited (sedentary: N = 17 or recreational: N = 14; mean age: 25.3 ± 4.4 years). After a fitness assessment on a cycle ergometer, subjects underwent three experimental conditions on separate days: high (20 min exercise 20% above lactate threshold), low (20 min exercise 20% below lactate threshold) and control (seated rest). Before and after each intervention Positive and Negative Affect Schedule, PTh and PTol (cold water emersion test) were assessed. Results Results indicate an increase of the Positive Affect Scale (high: 26.7 ± 9.0 vs. 32.9 ± 7.1, p < .001; low: 26.3 ± 7.2 vs. 32.0 ± 7.0, p < .001) and PTh (high: 45.1 ± 3.1°C vs. 46.0 ± 2.6°C, p = .003; low: 45.4 ± 2.7°C vs. 45.9 ± 2.6°C, p = .012) after both exercise conditions. In an exploratory analysis, PTol significantly increased only after the high exercise condition (51.2 ± 33.7 s vs. 72.4 ± 64.0 s, p = .045). Fitness level was positively correlated with the increase in PTol from pre to post high‐intensity exercise (r = .59, p (one‐tailed) = .002). Conclusion Exercise‐induced hypoalgesia depends on exercise intensity and appears to be influenced by individual fitness status, independent of mood responses. Significance Antinociceptive effects can be elicited by physical exercise and have been extensively investigated in the literature. However, the relation between exercise intensity, fitness status, and the degree of antinociception is not well‐understood. This randomized intervention provides novel evidence that antinociceptive effects indeed depend on exercise intensity, but also on general fitness status. Data extend the existing literature by highlighting aspects of exercise behaviour that promote antinociception. Effects do not simply mirror positive affective responses induced by exercise, hence, indicating partially distinct underlying mechanisms.