Thoracic spine manipulation has been shown to be effective for the management of neck pain. The purpose of this study was to investigate the immediate effect of a T3-T4 spinal thrust manipulation on autonomic nervous system activity in subjects with chronic cervical pain. An additional aim was to determine if the manipulation resulted in an immediate pain relief in patients with chronic neck pain when compared to a placebo intervention. One hundred subjects with chronic neck pain were randomly assigned to receive either a thoracic thrust manipulation or a placebo intervention. The Friedman's test was used to evaluate the change in pupil diameter within both groups. The Wilcoxen signed-ranks test was used to explore pupil changes over time and to make paired comparisons of the pupil change between the groups. The Mann-Whitney U test was used to compare the change in pain perception for the chronic cervical pain group subjects receiving either the thrust manipulation or the placebo intervention. The results demonstrated that manipulation did not result in a change in sympathetic activity. Additionally, there was no significant difference in the subject's pain perception (P = 0.961) when comparing the effects of the thrust manipulation to the placebo intervention within this group of subjects with chronic neck pain. The clinical impression of this study is that manipulation of the thoracic spine may not be effective in immediately reducing pain in patients with chronic neck pain.