Manual therapy (MT) and exercise therapy techniques are commonly utilised, guideline recommended treatment strategies in the management of non-specific low back pain (LBP). Preliminary evidence on asymptomatic participants indicates that two manual therapy techniques; repeated lumbar extension in lying exercise (EIL); and segmental rotational grade V manipulation (manipulation), have significant effects on the sympathetic nervous system (SNS) as detectable with skin conductance (SC) responses. However, it is not known if these responses occur in patients with LBP. A randomised, independent group's design was utilised to investigate the immediate SC responses in 50 patients with LBP of less than 12 weeks duration. Patients received either the manipulation technique (n = 25) or the EIL exercise (n = 25) and SC activity was recorded, in a single treatment session, pre-, peri- and post-treatment. Both treatments resulted in a sympatho-excitatory response during the intervention period with the manipulation technique having a 255% increase (p < 0.005), and the EIL technique a 94% increase (p = 0.019) with both treatments having responses that were sustained into the final rest period (p < 0.005). Between-group comparisons indicate that the manipulation technique had a significantly greater magnitude of effect (p < 0.001). The results support the sympatho-excitatory responses seen in normative studies but challenge the assumption that normative and patient populations are analogous with respect to the magnitude of effect observed and suggest that SC responses may be a feasible, proxy method of detecting dorsal horn sensitisation and neuro-plastic adaptations occurring in the presence of LBP.