BACKGROUND: Surgical resection remains the primary treatment for gastrointestinal (GI) malignancy including early-stage cancer. Omega-3 polyunsaturated fatty acids (n-3 PUFAs) have been reported to have beneficial clinical and immune-modulating effects in the prognosis of GI cancer patients undergoing surgery. METHODS: We searched PubMed, Embase, EBSCO-Medline, Cochrane Central Register of Controlled Trials (CENTRAL), CNKI and Wanfang to identify primary research reporting the effects of n-3 PUFAs compared with isocaloric nutrition on GI cancer patients who underwent surgery up to the end of June 30, 2016. Two authors independently reviewed and selected eligible randomized controlled trials (RCTs). RESULTS: A total of 9 RCTs (623 participants) were included. The n-3 PUFAs regime resulted in lower levels of C-reactive protein (CRP) (P < 0.05), interleukin-6 (IL-6) (P < 0.01), and higher levels of albumin (ALB), CD3(+) T cells, CD4(+) T cells and CD4(+)/CD8(+) ratio (P < 0.05) compared with the isocaloric nutrition regime. However, there was no significant difference in the level of tumor necrosis factor-α (TNF-α) between the n-3 PUFAs regime and the isocaloric nutrition regime (P = 0.17). And the level of CD8 (+) T cells decreased compared with the isocaloric nutrition regime (P < 0.0001). CONCLUSIONS: Our meta-analysis revealed that n-3 PUFAs are effective in improving the nutritional status and immune function of GI cancer patients undergoing surgery as they effectively enhance immunity and attenuate the inflammatory response.