Virtual reality (VR) is an appealing approach for increasing the engagement and attention of patients during rehabilitation. Understanding how motor control changes in real vs. virtual scenarios is a research challenge in terms of validating its administration. This study evaluates muscle synergies when subjects conduct throwing tasks in virtual reality. Seventeen healthy subjects performed 20 throws both in a virtual environment and in real one as they threw a ball with both dominant and nondominant arms. The electromyography (EMG) signals of 11 muscles of the upper limbs were recorded. Non-negative matrix factorization was used to extract muscle synergies. The cosine similarity was computed to assess the consistence of muscle synergy organization between virtual and real tasks. The same parameter was used to establish the inter-subject similarity. A three-synergy model was selected as the most likely. No effects of virtual reality and arm side on neuromuscular organization were found. Forearm muscles, not necessary for ball holding and release, were comprised in the activation synergies in the virtual reality environment. Finally, the synergies were consistent across subjects, especially during the deceleration phase. Results are encouraging for the application of virtual reality to complement conventional therapy, improve engagement, and facilitate objective measurements of pathology progression.