Certain secondary effects derived from medical treatment in breast cancer can favor the development of alterations in shoulder biomechanics. To the best of our knowledge, persistent peripheral pain as a key factor for the development of neuromuscular activity impairments has not been analyzed. A cross-sectional descriptive study was carried out. A total of 90 women were included and allocated to three groups: (i) 30 women with persistent peripheral pain after breast cancer treatment, (ii) 30 women without pain after breast cancer treatment, and (iii) 30 healthy women. Surface electromyography was employed to measure the onset and amplitude of the muscle activity of three shoulder movements. Statistically significant differences were found in the neuromuscular activity for all the muscles and shoulder movements among women with persistent pain versus healthy women (i.e., amplitude muscle activity variable p < 0.001). Statistically significant differences were also observed in the neuromuscular activity for certain muscles in shoulder movements among women with persistent pain versus women without pain, as well as between women without pain versus healthy women. Therefore, following breast cancer treatment, women showed alterations in their shoulder neuromuscular activity, which were more significant if persistent pain existed. These findings may contribute to developing a selective therapeutic exercise program that optimizes the shoulder neuromuscular activity in women after breast cancer treatment.