Arthrogryposis multiplex congenita (AMC) has recently drawn substantial attention from researchers and clinicians. New effective surgical and physiotherapeutic methods have been developed to improve the quality of life of patients with AMC. While it is clear that all these interventions should strongly rely on the plastic reorganization of the central nervous system, almost no studies have investigated this topic. The present study demonstrates the feasibility of using magnetoencephalography (MEG) to investigate brain activity in young AMC patients. We also outlined the general challenges and limitations of electrophysiological investigations on patients with arthrogryposis. We conducted MEG recordings using a 306-channel Elekta Neuromag VectorView system during a cued motor task performance in four patients with arthrogryposis, five normally developed children, and five control adults. Following the voice command of the experimenter, each subject was asked to bring their hand toward their mouth to imitate the self-feeding process. Two patients had latissimus dorsi transferred to the biceps brachii position, one patient had a pectoralis major transferred to the biceps brachii position, and one patient had no elbow flexion restoration surgery before the MEG investigation. Three patients who had undergone autotransplantation prior to the MEG investigation demonstrated activation in the sensorimotor area contralateral to the elbow flexion movement similar to the healthy controls. One patient who was recorded before the surgery demonstrated subjectively weak distributed bilateral activation during both left and right elbow flexion. Visual inspection of MEG data suggested that neural activity associated with motor performance was less pronounced and more widely distributed across the cortical areas of patients than of healthy control subjects. In general, our results could serve as a proof of principle in terms of the application of MEG in studies on cortical activity in patients with AMC. Reported trends might be consistent with the idea that prolonged motor deficits are associated with more difficult neuronal recruitment and the spatial heterogeneity of neuronal sources, most likely reflecting compensatory neuronal mechanisms. On the practical side, MEG could be a valuable technique for investigating the neurodynamics of patients with AMC as a function of postoperative abilitation.