The impact of chronic pelvic pain syndrome on sexual function in men is underestimated. We quantified sexual dysfunction (ejaculatory pain, decreased libido, erectile dysfunction and ejaculatory difficulties) in men with chronic pelvic pain syndrome and assessed the effects of pelvic muscle trigger point release concomitant with paradoxical relaxation training. We treated 146 men with a mean age of 42 years who had had refractory chronic pelvic pain syndrome for at least 1 month with trigger point release/paradoxical relaxation training to release trigger points in the pelvic floor musculature. The Pelvic Pain Symptom Survey and National Institutes of Health-Chronic Prostatitis Symptom Index were used to document the severity/frequency of pain, urinary and sexual symptoms. A global response assessment was done to record patient perceptions of overall therapeutic effects at an average 5-month followup. At baseline 133 men (92%) had sexual dysfunction, including ejaculatory pain in 56%, decreased libido in 66%, and erectile and ejaculatory dysfunction in 31%. After trigger point release/paradoxical relaxation training specific Pelvic Pain Symptom Survey sexual symptoms improved an average of 77% to 87% in responders, that is greater than 50% improvement. Overall a global response assessment of markedly or moderately improved, indicating clinical success, was reported by 70% of patients who had a significant decrease of 9 (35%) and 7 points (26%) on the National Institutes of Health-Chronic Prostatitis Symptom Index (p < 0.001). Pelvic Pain Symptom Survey sexual scores improved 43% with a markedly improved global response assessment (p < 0.001) but only 10% with moderate improvement (p = 0.96). Sexual dysfunction is common in men with refractory chronic pelvic pain syndrome but it is unexpected in the mid fifth decade of life. Application of the trigger point release/paradoxical relaxation training protocol was associated with significant improvement in pelvic pain, urinary symptoms, libido, ejaculatory pain, and erectile and ejaculatory dysfunction.