Understanding the kinematics of the upper extremity during kayak paddling is important for both performance and injury prevention. However, there is a lack of information on scapular and shoulder kinematics in para-kayakers who have additional impairments. This study aimed to clarify the biomechanics of kayak paddling in para-kayakers. We assessed the biomechanics of 5 para-kayakers (included the subjects who competed the 2016 Rio Paralympic Games) and 10 elite able-bodied kayakers (included the subjects who competed the London Olympic Games in 2012 or world championships) during paddling on a kayak ergometer using an electromagnetic tracking device. The stroke rate, scapular motion relative to thorax, humerus motion relative to thorax, and humerus motion relative to scapula during the first 10 cycles of paddling were evaluated. During the first 10 cycles of paddling, para-kayakers showed significantly lower stroke rate compared to elite kayakers. There were also significant differences in scapular upward/downward rotation, humerothoracic plane of elevation, and grenohumeral plane of elevation between the para-kayakers and the elite kayakers. Para-kayakers who have some impairments showed lower kayak paddling performance and different movement patterns compared with elite kayakers. The results of this study could provide some information to guide training programs to improve para-kayakers’ performance.