Experimental pain is known to affect neuroplasticity of the motor cortex as well as motor performance, but less is known about neuroplasticity of somatosensory processing in the presence of pain. Early somatosensory evoked potentials (SEPs) provide a mechanism for investigating alterations in sensory processing and sensorimotor integration (SMI). The overall aim of this study was to investigate the interactive effects of acute pain, motor training, and sensorimotor processing. Two groups of twelve participants (N = 24) were randomly assigned to either an intervention (capsaicin cream) or placebo (inert lotion) group. SEP amplitudes were collected by stimulation of the median nerve at baseline, post-application and post-motor training. Participants performed a motor sequence task while reaction time and accuracy data were recorded. The amplitude of the P22-N24 complex was significantly increased following motor training for both groups F(2,23) = 3.533, p < 0.05, while Friedman's test for the P22-N30 complex showed a significant increase in the intervention group [χ(2) (df = 2, p = 0.016) = 8.2], with no significant change in the placebo group. Following motor training, reaction time was significantly decreased for both groups F(1,23) = 59.575, p < 0.01 and overall accuracy differed by group [χ(2) (df = 3, p < 0.001) = 19.86], with post hoc testing indicating that the intervention group improved in accuracy following motor training [χ(2) (df = 1, p = 0.001) = 11.77] while the placebo group had worse accuracy [χ(2) (df = 1, p = 0.006) = 7.67]. The improved performance in the presence of capsaicin provides support for the enhancement of knowledge acquisition with the presence of nontarget stimuli. In addition, the increase in SEP peak amplitudes suggests that early SEP changes are markers of SMI changes accompanying motor training and acute pain.