Muscle tenderness has been measured in several studies to evaluate effectiveness of treatment methods, but only short-term results have been reported so far. The aim of the present study was to evaluate the long-term effects of two different muscle training methods on the pressure pain threshold of neck muscles in women with neck pain. Altogether 180 woman with chronic, non-specific neck pain were randomized into three groups: neck muscle endurance training, neck muscle strength training and control groups. The main outcome measures included pressure pain threshold measurement at six muscle sites and on the sternum. Neck pain was assessed by a visual analogue scale (VAS). At the 12-month follow-up statistically significantly higher pressure pain threshold values were obtained in both training groups at all muscle sites compared to the baseline, while no significant change occurred in the controls. Significantly higher changes in pressure pain threshold were detected at all six sites in the strength training group and at four out of six sites in the endurance training group compared to the control group. This is the first study to show an increase in pressure pain thresholds as a result of long-term muscle training. A decrease in neck pain was associated with reduced pressure pain sensitivity in neck muscles, showing that the pressure pain threshold may be a useful outcome measure of the effectiveness of neck muscle rehabilitation.