We assessed the effects of a 3-min partial-body cryostimulation (PBC) exposure—where the whole body is exposed to extreme cold, except the head—on cognitive inhibition performance and the possible implications of parasympathetic cardiac control and cerebral oxygenation. In a randomized controlled counterbalanced cross-over design, eighteen healthy young adults (nine males and nine females) completed a cognitive Stroop task before and after one single session of PBC (3-min exposure at − 150 °C cold air) and a control condition (3 min at room temperature, 20 °C). During the cognitive task, heart rate variability (HRV) and cerebral oxygenation of the prefrontal cortex were measured using heart rate monitoring and near-infrared spectroscopy methods. We also recorded the cerebral oxygenation during the PBC session. Stroop performance after PBC exposure was enhanced (562.0 ± 40.2 ms) compared to pre-PBC (602.0 ± 56.4 ms; P < 0.042) in males only, accompanied by an increase ( P < 0.05) in HRV indices of parasympathetic tone, in greater proportion in males compared to females. During PBC, cerebral oxygenation decreased in a similar proportion in males and females but the cerebral extraction (deoxyhemoglobin: $Δ$HHb) remained higher after exposure in males, only. These data demonstrate that a single PBC session enhances the cognitive inhibition performance on a Stroop task in males, partly mediated by a greater parasympathetic cardiac control and greater cerebral oxygenation. The effects of PBC on cognitive function seem different in females, possibly explained by a different sensitivity to cold stimulation.