This case report introduces an innovative and novel way of functionally retraining the sport specific cervical function in a 13-year-old elite water polo player with a combined tension type headache and cervicogenic headache. After an evidence based assessment and manipulative physical therapy management regime, consisting of manual mobilization and exercise focused on retraining the deep cervical flexors and sub-occipital extensors, the patient was left with persistent residual complaints inhibiting competitive level sport participation. Re-assessment and subsequent retraining of a specific provocative functional task was facilitated by using the Cervical Trainer(™). Using a wireless sensor worn on the head, this device registers three-dimensional movement and displays this on a computer screen, providing direct feedback on movement performance. After a 6-week period of training sessions, the residual complaints subsided and her score on the Headache Impact Test-6 questionnaire improved from 51 to 36 signifying no impact of her headache on daily life activities.