Pain is associated with changes in the neural drive to muscles. For the upper trapezius muscle, surface EMG recordings have indicated that acute noxious stimulation in either the cranial or the caudal region of the muscle leads to a relative decrease in muscle activity in the cranial region. It is however not known if this adaption reflects different recruitment thresholds of the upper trapezius motor units in the cranial and caudal region or a non-uniform nociceptive input to the motor units of both regions. This study investigated these potential mechanisms by direct motor unit identification. Motor unit activity was investigated with high-density surface EMG signals recorded from the upper trapezius muscle of 12 healthy volunteers at baseline, control (intramuscular injection of isotonic saline), and painful condition (hypertonic saline). The EMG was decomposed into individual motor unit spike trains. Motor unit discharge rates decreased significantly from control to pain conditions by 4.0 ± 3.6 pps in the cranial region but not in the caudal region (1.4 ± 2.8 pps; not significant). These changes were compatible with variations in the synaptic input to the motor neurons of the two regions. These adjustments were observed irrespective of the location of noxious stimulation. These results strongly indicate that the nociceptive synaptic input is distributed in a non-uniform way across regions of the upper trapezius muscle.