Objectives A systematic review and meta‐analysis of the literature was conducted to compare the accuracy with which flexible endoscopic evaluation of swallowing (FEES) and videofluoroscopic swallowing study (VFSS) assessed oropharyngeal dysphagia in adults. Data Sources PubMed, Embase, and the Latin American and Caribbean Health Sciences Literature (LILACS) database. Methods A review of published studies was conducted in parallel by two groups of researchers. We evaluated the methodological quality, homogeneity, threshold effect, and publication bias. The results are presented as originally published, then with each test compared against the other as a reference and both compared against a composite reference standard, and then pooled using a random effects model. Software use consisted of Meta‐DiSc and SPSS. Results The search yielded 5,697 articles. Fifty‐two articles were reviewed in full text, and six articles were included in the meta‐analysis. FEES showed greater sensitivity than VFSS for aspiration (0.88 vs. 0.77; P = .03), penetration (0.97 vs. 0.83; P = .0002), and laryngopharyngeal residues (0.97 vs. 0.80; P < .0001). Sensitivity to detect pharyngeal premature spillage was similar for both tests (VFSS: 0.80; FEES: 0.69; P = .28). The specificities of both tests were similar (range, 0.93–0.98). In the sensitivity analysis there were statistically significant differences between the tests regarding residues but only marginally significant differences regarding aspiration and penetration. Conclusions FEES had a slight advantage over VFSS to detect aspiration, penetration, and residues. Prospective studies comparing both tests against an appropriate reference standard are needed to define which test has greater accuracy. Level of Evidence 2a Laryngoscope , 127:2002–2010, 2017