Deep cervical flexor muscle (DCF) activation is impaired with neck pain. This study investigated the effects of low load cranio-cervical flexion (C-CF) and neck flexor strengthening exercises on spatial and temporal characteristics of DCF activation during a neck movement task and a task challenging the neck's postural stability. Forty-six chronic neck pain subjects were randomly assigned to an exercise group and undertook a 6-week training program. Electromyographic (EMG) activity was recorded from the DCF, sternocleidomastoid (SCM) and anterior scalene (AS) muscles pre and post intervention during the cranio-cervical flexion test (CCFT) and during perturbations induced by rapid, unilateral shoulder flexion and extension. C-CF training increased DCF EMG amplitude and decreased SCM and AS EMG amplitude across all stages of the CCFT (all P<0.05). No change occurred in DCF EMG amplitude following strength training. There was no significant between group difference in pre-post intervention change in relative latency of DCF but a greater proportion of the C-CF group shortened the relative latency between the activation of the deltoid and the DCF during rapid arm movement compared to the strength group (P<0.05). Specific low load C-CF exercise changes spatial and temporal characteristics of DCF activation which may partially explain its efficacy in rehabilitation.