The aims of this study were to compare and analyze two types of deep cervical flexion exercises, craniocervical flexion and cervical flexion, and to ascertain their relative effects on neck and shoulder pain and functional improvement. The participants of the study were individuals who work in sedentary jobs in an office environment. 54 appropriate subjects were chosen and randomly divided into two groups: one group underwent a craniocervical flexion exercise program and the other a cervical flexion exercise program. The six week exercise program consisted of home exercises performed by each subject five times a week and education once a week. Neck-shoulder pain, muscle strengthening, cervical alignment were measured prior to commencement of the exercise programs and again after six weeks. At completion of the six week, both exercise programs decreased neck pain (p<.05). Forward head postures were reduced, and the craniocervical flexion exercise program was more effective in reducing forward head posture (p<.05). The maximum muscle strength and 50% of maximum muscle strength maintaining time of the deep cervical flexor muscles were significantly increased. There were no significant changes of the cervical lordotic curve. The results of this study showed deep cervical flexion exercise was effective in the treatment of neck and shoulder pain, however craniocervical flexion exercise was more effective than cervical flexion exercise.