The INYBI is an instrument used to release the suboccipital myofascial area. There is scarce evidence of its efficacy. A randomized controlled, double-blinded, longitudinal and prospective trial was performed. Ninety-six subjects (aged 29.47 ± 5.16 years) (70 women) with chronic neck pain were randomly assigned to the manual suboccipital inhibition technique (MSIT), instrumental suboccipital inhibition (INYBI) or the INYBI plus upper cervical manipulation technique (INYBI + UCMT) groups and received two sessions with a week interval between them. The Neck Disability Index was used before the first intervention and two weeks after the second intervention. Pre- and post-measurements were taken on both intervention days for pressure pain threshold of the upper trapezius and suboccipital muscles, self-perceived pain and cervical range of motion. In spite of a significant general improvement in time that was found for the three groups for all of the outcome measurements (p < 0.05 in all cases), no between-groups differences were found (p > 0.05 in all cases), with the exception of self-perceived pain for left rotation (p = 0.024), with the MSIT group showing the lower improvement. However, the higher degree of within-group improvements was found for the INYBI + UCMT group. It was concluded that the myofascial release therapy in the suboccipital area is effective in patients with chronic neck pain, either through a manual application or by means of the INYBI tool. Moreover, the addition of craniocervical manipulation achieved the higher within-group improvements, but with no statistical significance.