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This study investigated the impact of stroke on the control of upper limb endpoint force during isokinetic exercise, a dynamic force-generating task, and its association with stroke-affected muscle synergies. Three-dimensional upper limb endpoint force and electromyography of shoulder and elbow muscles were collected from sixteen chronic stroke survivors and eight neurologically intact adults. Participants were instructed to control the endpoint force direction during three-dimensional isokinetic upper limb movements. The endpoint force control performance was quantitatively evaluated in terms of the coupling between forces in orthogonal directions and the complexity of the endpoint force. Upper limb muscle synergies were compared between participants with varying levels of endpoint force coupling. The stroke survivors generating greater force abnormality than the others exhibited interdependent activation profiles of shoulder- and elbow-related muscle synergies to a greater extent. Based on the relevance of synergy activation to endpoint force control, this study proposes isokinetic training to correct the abnormal synergy activation patterns post-stroke. Several ideas for implementing effective training for stroke-affected synergy activation are discussed.