Sexual dysfunction and psychological distress are common after prostate cancer. Research has not examined the role of neuroendocrine markers of stress (e.g. cortisol). This study examines whether sexual functioning or sexual bother is associated with diurnal cortisol. Men treated for prostate cancer completed the University of California-Los Angeles Prostate Cancer Index and provided saliva samples four times daily for cortisol assessment. Higher sexual bother, but not sexual functioning, was associated with steeper cortisol slope. Better sexual functioning, and not sexual bother, was significantly associated with the cortisol awakening response. Assessment of stress and stress-reducing interventions might be warranted in sexual rehabilitation after prostate cancer.