Both low-load and high-load training of the cervical muscles have been shown to reduce neck pain and change parameters of muscle function directly related to the exercise performed. The purpose of this study was to investigate whether either training regime changes muscle activation during a functional task which is known to be affected in people with neck pain and is not directly related to either exercise protocol. Fifty-eight female patients with chronic neck pain were randomised into one of two 6-week exercise intervention groups: an endurance-strength training regime for the cervical flexor muscles or low-load training of the cranio-cervical flexor muscles. The primary outcome was a change in electromyographic (EMG) amplitude of the sternocleidomastoid (SCM) muscle during a functional, repetitive upper limb task. At the 7th week follow-up assessment both intervention groups demonstrated a reduction in their average intensity of pain (P<0.05). However, neither training group demonstrated a change in SCM EMG amplitude during the functional task (P>0.05). The results demonstrate that training the cervical muscles with a prescribed motor task may not automatically result in improved muscle activation during a functional activity, despite a reduction in neck pain.