Background and aims Poststroke shoulder pain is a common complication. We aimed to investigate the prevalence of poststroke shoulder pain, with attention to the neuropathic component, and the relationship between poststroke shoulder pain and upper limb improvement in motor function, strength, disability, and quality of life after upper limb rehabilitation. Methods This is a secondary analysis of a multicenter randomized controlled trial to compare upper limb conventional or robotic rehabilitation on 224 patients enrolled in eight rehabilitation centers. We assessed poststroke shoulder pain (using the Numerical Rating Scale and the Douleur Neuropathique 4), and upper limb motor function, strength, disability, and quality of life at baseline (T0), after 30 rehabilitation sessions (T1), and three months after the end of rehabilitation (T2). Results A moderate/severe poststroke shoulder pain was reported by 28.9% of patients, while 19.6% of them showed a neuropathic component. At T0, the intensity of pain was higher in women and in patients with neglect syndrome, positively correlated with the time since stroke and disability and negatively correlated with motor function, strength, and the physical aspects of the quality of life. Moderate/severe pain and neuropathic component significantly reduced after both treatments and this reduction was maintained at T2. Finally, the intensity of pain at baseline was negatively correlated with the improvement of upper limb motor function. Conclusions Poststroke shoulder pain negatively impact on motor performance, strength, disability, and physical aspects of the quality of life as well as on upper limb motor recovery; however, it can be reduced after a robotic or a conventional rehabilitation. Therefore, we suggest considering poststroke shoulder pain when planning the rehabilitation intervention.