We need to understand more about how DNF performs in different contexts and whether it affects the pain threshold over myofascial trigger points (MTrPs). The objectives were to investigate the effect of neck muscles training on disability and pain and on pain threshold over MTrPs in people with chronic neck pain. Patients with chronic neck pain were eligible for participation with a Neck Disability Index (NDI) score of over 5/50 and having at least one MTrP on either levator scapulae, upper trapezoid, or splenius capitis muscle. Patients were randomly assigned into either DNF training, superficial neck muscle exercise, or advice group. Generalized linear model (GLM) was used to detect differences in treatment groups over time. Out of 67 participants, 60 (47 females, mean age: 39.45 ± 12.67) completed the study. Neck disability and neck pain were improved over time between and within groups ( < 0.05). However, no differences were found within and between the therapeutic groups ( < 0.05) in the tested muscles' PPTs and in cervicothoracic angle over a 7-week period. All three groups improved over time. This infers that the pain pathways involved in the neck pain relief are not those involved in pain threshold.