Context Shoulder and neck pain are leading causes of disability worldwide. Rotator cuff pathology has strong associations with such pain and is extensively targeted by healthcare practitioners. A dysfunctional lower trapezius muscle has also been shown to contribute to neck and shoulder pain, yet it is often overlooked. Objectives This systematic review analyzes those with a history of, or who are currently managing, shoulder or neck pain to indicate differences in measures of lower trapezius function when compared to subjects without that pain. Methods Studies with no age restrictions were included in the study. Studies could determine lower trapezius muscle function with any quantifiable measurement tool or clinical assessment. If the study included a control group (no pain) and a comparator group (pain), and if lower trapezius muscle function was assessed in both, the study was typically included. The significance of the lower trapezius muscle function change was summarized in these pain patients. From a final total of 18 studies identified, level of muscle activity, muscle activation, time to onset, muscle strength, and muscle thickness were reported. Results The 18 included articles involved 485 participants with shoulder and/or neck pain and 455 without. Half of the shoulder pain studies (6/12), and all of the neck pain studies (6/6), demonstrated that the lower trapezius had a noticeable impact. The lower trapezius muscle in participants with shoulder and neck pain tended to show decreased muscle strength, and decreased time to onset/latency. Conclusions The findings from this systematic review should be taken into consideration when assessing and treating patients with shoulder and neck pain. Future studies that define the type and duration of shoulder and neck pain, as well as prospectively assessing lower trapezius muscle function in those with and without that pain, are needed.