The present study aims at studying interactions between cognitive performance and conditioned pain modulation in patients with chronic whiplash-associated disorders (WAD) and healthy controls. In addition, the relation between cortisol concentrations and cognitive performance will be studied in patients with chronic WAD. Thirty-one subjects, 16 healthy subjects and 15 patients with chronic WAD, were enrolled and subjected to several self-report and physiological measures. Self-report measures encompassed pain rating during a procedure evaluating conditioned pain modulation. Afterward, they were subjected to physiological measures, which are cognitive tests (Stroop task, psychomotor vigilance task, and operation span task) preceded and followed by salivary cortisol concentration measurements. Chronic WAD patients performed worse in recall at the operation span task and presented longer reaction times at the psychomotor vigilance task and at the Stroop task when sleep-related words were shown (p < .05). Conditioned pain modulation and cortisol concentrations were not significantly different between patients and controls (p > .05). Only in the healthy subjects, conditioned pain modulation and baseline cortisol concentrations were correlated to cognitive performance (p < .05). This is the first study addressing the relation between pain inhibition and cognitive performance in chronic WAD. We did not reveal impaired pain inhibition but did reveal cognitive dysfunctions in patients with chronic WAD. In healthy subjects, pain inhibition was related to cognitive performance but not in the patient group.