The primary aim of this was to assess the effectiveness of stretching for improving shoulder range of motion (ROM) in overhead athletes with glenohumeral internal rotation deficit (GIRD). The secondary aims were to compare whether the combination of stretching plus manual therapy was more effective than stretching in isolation and if any stretching technique was superior to others. A systematic review and a meta-analysis were designed. The MEDLINE, PEDro, Cochrane Library, and Web of Science databases were searched. Clinical trials investigating the effects of stretching in isolation or combined with other manual therapy techniques on ROM and pain intensity in athletes with GIRD were included. The PEDro scale was used to assess the methodological quality of the studies, and the certainty of evidence was assessed using the GRADE tool. Two independent assessors extracted data through a standardized form. The random-effects models were applied. Sixteen randomized controlled trials were included in this systematic review with a meta-analysis, with a methodological quality ranging from high to low. The stretching techniques in isolation showed statistically significant improvements in internal rotation and horizontal adduction ROM. Adding glenohumeral dorsal gliding to a stretching protocol showed better improvement in internal rotation ROM than stretching in isolation. Stretching techniques with manual stabilization showed better benefits than self-stretching techniques. A very low certainty of evidence suggests that stretching produces statistically significant changes for improving ROM in patients with glenohumeral internal rotation deficit. The combination with glenohumeral dorsal gliding seems to produce better improvements.