Purpose Prognostic significance of fluorine-18 fluorodeoxyglucose positron emission tomography (18F-FDG-PET) in anal squamous cell carcinoma (SCC) has been evaluated in several studies; however, the results seem to be controversial and no consensus exists about its predictive capability. The current meta-analysis was carried out to comprehensively investigate the prognostic significance of 18F-FDG-PET parameters in patients with anal SCC. Methods A comprehensive literature search of PubMed/MEDLINE and Scopus databases was performed to retrieve pertinent articles published until August 5th 2018, concerning the prognostic significance of 18F-FDG-PET in patients with anal SCC. No language restriction was used. Several prognostic factors were reported for progression-free survival (PFS) and overall survival (OS) including pretreatment maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), inguinal nodal uptake, and metabolic response to therapy. Results Eleven studies (741 patients) were included. The pooled hazard ratio (HR) for the probability of PFS was 5.36 (95% confidence interval (95% CI): 3.12–9.21, p < 0.001) for metabolic response to therapy and 1.98 (95% CI: 1.26–3.12, p=0.003) for SUVmax. The pooled HR for the probability of OS was 5.87 (3.02–11.39, p < 0.0001) for metabolic response to therapy. On the other hand, the study revealed that the pooled HRs of MTV and inguinal nodal uptake for PFS were 1.56 (95% CI: 0.96–2.53, p=0.072) and 1.79 (95% CI: 1–3.21, p=0.051), respectively. Conclusions Our findings propose that some 18F-FDG-PET parameters could serve as prognostic indicators in anal SCC, but further larger studies are needed in this setting.