Muscle pain induces a complex reorganization of the motor strategy which cannot be fully explained by current theories. We tested the hypothesis that the neural control of muscles during reaching in the presence of nociceptive input is determined by a reorganization of muscle synergies with respect to control conditions. Muscle pain was induced by injection of hypertonic saline into the anterior deltoid muscle of eight men. Electromyographic (EMG) signals were recorded from 12 upper limb muscles as subjects performed a reaching task before (baseline) and after the injection of hypertonic (pain) saline, and after the pain sensation vanished. The EMG envelopes were factorized in muscle synergies, and activation signals extracted for each condition. Nociceptive stimulation resulted in a complex muscle reorganization without changes in the kinematic output. The anterior deltoid muscle activity decreased in all subjects while the changes in other muscles were subject specific. Three synergies sufficed to describe the EMG patterns in each condition, suggesting that reaching movements remain modular in the presence of experimental pain. Muscle reorganization in all subjects was accompanied by a change in the activation signals compatible with a change in the central drive to muscles. One, two or three synergies were shared between the baseline and painful conditions, depending on the subject. These results indicate that nociceptive stimulation may induce a reorganization of modular control in reaching. We speculate that such reorganization may be due to the recruitment of synergies specific to the painful condition.