Head and Neck Cancer (HNC) is a globally rare cancer that includes a variety of tumors affecting the upper aerodigestive tract. It presents with difficulty breathing or swallowing and is mainly treated with radiation therapy, chemotherapy, or surgery for tumors that have spread locally or throughout the body. Alternatively, exercise can be used during cancer treatment to improve function, including pain relief, increase range of motion and muscle strength, and reduce cancer-related fatigue, thereby enhancing quality of life. Although existing evidence suggests the adjunctive use of exercise in other cancer types, no previous studies have examined the effects on HNC survivors. The aim of this meta-analysis was to quantify the effect of exercise-based rehabilitation on functionality and quality of life in HNC survivors who underwent surgery and/or chemoradiotherapy. A systematic review and meta-analysis were carried out following PRISMA statement and registered in PROSPERO (CRD42023390300). The search was performed in MEDLINE (PubMED), Cochrane Library, CINAHL and Web of Science (WOS) databases from inception to 31st December 2022 using the terms “cancer”, “head and neck neoplasms”, “exercise”, “rehabilitation”, “complications”, “muscle contraction”, “muscle stretching exercises” combining with booleans “AND”/“OR”. PEDro scale, Cochrane Risk of Bias Tool and GRADE were used to assess methodological quality, risk of bias and grade of recommendation of included studies respectively. 18 studies (n = 1322) were finally included which 1039 (78.6%) were men and 283 (21.4%) were women. In patients who underwent radio-chemotherapy, overall pain [SMD = − 0.62 [− 4.07, 2.83] CI 95%, Z = 0.35, p = 0.72] and OP [SMD = − 0.07 [− 0.62, 0.48] CI 95%, Z = 0.25, p = 0.81] were slightly reduced with exercise in comparison to controls. Besides, lower limb muscle strength [SMD = − 0.10 [− 1.52, 1.32] CI 95%, Z = 0.14, p = 0.89] and fatigue [SMD = − 0.51 [− 0.97, − 0.057] CI 95%, Z = 2.15, p < 0.01] were also improved in those who receive radio-chemoradiation. In HNC survivors treated with neck dissection surgery, exercise was superior to controls in overall pain [SMD = − 1.04 [− 3.31, 1.23] CI 95%, Z = 0.90, p = 0.37] and, in mid-term, on shoulder pain SMD = − 2.81 [− 7.06, 1.43] CI 95%, Z = 1.76, p = 0.08]. No differences in quality of life were found at any of the follow-up periods. There is evidence of fair to good methodological quality, low to moderate risk of bias, and weak recommendations supporting the use of exercise-based rehabilitation to increase functionality. However, no evidence was found in favor of the use of this modality for improving the quality of life of HNC survivors who underwent chemoradiotherapy or surgery.