The objective of this study was to investigate and to determine the effectiveness of specific Stability Exercises (SE)on the muscles of the neck in comparison with Proprioceptive Neuromuscular Facilitation exercises (PNFE) in the cross-sectional area of deep cervical flexor muscles and to examine the improvement of disability and pain in patients with chronic neck pain. This randomized controlled clinical trial was conducted on 44 patients with chronic neck pain in 2016. The patients were randomly divided into two SE and (PNFE) groups (each containing 22 subjects). The pain of patients was assessed using VisualAnalogScale(VAS) questionnaire(VAS) and the disability was assessed using Neck Disability Index(NDI)questionnaire, and cross-sectional area of deep cervical flexor muscles in the right side was assessed using ultrasonography before treatment training and 8 weeks after the start of training. Treatment program for both groups was 8 weeks (6 sessions per week and two sessions per day) with repetition of specified trainings. Variance analysis, independent t-test, and paired t-test were used to compare results before and after treatment between groups and within groups .The mean pain score in both SE (P<0.001) and PNFE (P<0.001) groups was declined. Mean NDI in both SE (P<0.001) and PNFE (P<0.001) groups showed a significant decrease. The mean cross-sectional area of deep cervical flexor muscles of patients in SE group and PNFE group increased while the increase in PNFE group (P=0.09) was not significant but in SE group was statistically significant (P=0.008).This study revealed that both methods of SE and PNFE in patients with chronic neck pain reduced pain and disability, but SE had better effects. Although cross-sectional area of deep cervical flexor muscles increased in both treatment groups, but the increase in cross-sectional area of deep flexor muscles in SE group was significant.