Abstract Background It is generally accepted that microRNA-20a (miR-20a) is aberrantly expressed in gastrointestinal cancer (GIC), and may be associated with the prognosis of GIC patients. Nevertheless, the clinical prognostic value of miR-20a expression in GIC remains controversial. Methods We first conducted a comprehensive literature search of the clinical data and pooled them for evidence in assessing prognostic significance of miR-20a expression in GIC. Afterwards, we applied some bioinformatic analysis methods to explore the biological function of miR-20a and explain why miR-20a could act as an effective biomarker. Results The pooled results showed that enhanced miR-20a expression was significantly associated with poor survival in GIC patients (HR: 1.36; 95%CI: 1.21–1.52; P < 0.001). According to the subgroup analysis, the ethnicity, cancer type, sample source, and sample size may have an impact on the predictive roles for miR-20a. The gene ontologies enriched by the predicted miR-20a targets were highly associated with some important biological processes, cell components and molecular functions. Moreover, a series of prominent pathways linked with GIC carcinogenesis were identified. Ultimately, the crucial targets and modules were identified by constructing the protein-protein interaction network of miR-20a targets, which were highly associated with the initiation and progression of GIC according to previous molecular biology experiments. Conclusions Our results indicated that high expression of miR-20a may be a credible indicator of worse prognosis in GIC. Further studies involving biological experiments and larger sample sizes should be performed to validate these findings. Keywords: Gastrointestinal cancer, microRNA-20a, Prognosis prediction, Function exploration Background Gastrointestinal cancer (GIC), one of the most common malignancies, has overtaken cardiovascular disease and infectious diseases as a significant health burden with the leading cause of mortality across the world because of the growing incidence each year and poor prognosis [[35]1]. Although diagnostic and therapeutic strategies for GICs have been greatly improved, the prognosis of these patients remains very unsatisfying according to the latest statistics [[36]2]. Currently, TNM stage-based predictive system and some markers such as CEA play important roles in the monitoring and prognosis of GIC. However, there is still no effective biological biomarkers to understand the cancer development and tumor behavior and promote more precise risk stratification, as well as optimal choice of therapy [[37]3]. Hence, it is urgently needed to explore new credible prognostic markers which could be applied to supplement the current TNM stage-based predictive system and to provide guidance for cancer therapy. The microRNAs are small single-stranded RNA molecules that mediate the downstream gene expression in a post-transcriptional manner [[38]4]. An increasing number of recent studies have emphasized the roles of microRNAs in a variety of biological activities such as proliferation, apoptosis, angiogenesis, invasion, and migration [[39]5]. Due to its stability and detectability in tissues and blood, microRNAs might function as promising biomarkers for cancer early diagnosis, prognosis or treatment responses prediction [[40]6]. Notably, miR-20a stands out as the most investigated example in functional microRNAs. Recently published work has implicated its significant function in cancer pathogenesis and during the initiation and progression processes of carcinogenesis [[41]7]. Furthermore, accumulating new evidence demonstrates that aberrant expression of miR-20a may be highly associated with initiation and metastasis in GIC [[42]8]. Nevertheless, there are inconsistencies regarding the prognostic value of miR-20a in GIC, though a large number of studies reported associations between miR-20a expression and the clinical outcomes [[43]9]. Thus, through a comprehensive literature search of the relevant studies, we conducted an integrated meta-analysis regarding the influence of miR-20a expression level on overall survival of GIC patients. Additionally, functional exploration by bioinformatic analysis was performed to provide a better understanding of the prognostic significance for miR-20a involved in the occurrence and development of GIC, aiming to provide more theoretical supports for targeted treatment. Methods Literature retrieval strategy Two researchers (QP and PZ) independently conducted a systematic computerized literature search for available studies in selected electronic databases of PubMed, EMBASE and Web of science until October 2019. Search keywords were (microRNA-20a OR miR-20a OR miR20a OR miRNA-20a OR miRNA20a) AND (colorectal OR colon OR rectal OR rectum OR gastric OR gastrointestinal OR stomach) AND (tumor OR neoplasm OR cancer OR carcinoma OR malignancy). We also retrieved studies by hands from other potentially qualified publications to complement the results including relevant meta-analyses, reviews and references cited in these