Background Glenohumeral joint instability is associated with structural deficits and/or alterations in sensory and motor processing; however, a proportion of patients with glenohumeral joint instability fail to respond to surgical and rehabilitative measures. This systematic review aimed to establish if functional cortical changes occur in patients with glenohumeral joint instability. Methods AMED, CINAHL, Cochrane Central Register of Controlled Trials, Embase, Medline, PEDro, Pubmed, PsychINFO and Scopus were searched from inception to 17 March 2021. Randomised controlled trials and non-randomised trials were included and quality was appraised using the Downs and Black tool. Results One thousand two hundred seventy-nine records were identified of which five were included in the review. All studies showed altered cortical function when comparing instability patients with healthy controls and included areas associated with higher cortical functions. Discussion The findings of this systematic review offer some insight as to why interventions addressing peripheral pathoanatomical factors in patients with glenohumeral joint instability may fail in some cases due to functional cortical changes. However, data are of moderate to high risk of bias. Further high-quality research is required to ascertain the degree of functional cortical changes associated with the type and duration of glenohumeral joint instability.