The current guidelines on branch duct type intraductal papillary mucinous neoplasm (BD-IPMN) recommend various predictive features of malignancy as well as different treatment strategies. This study aimed to identify the risk factors for malignancy with higher level of evidence. A meta-analysis was performed on 40 literatures published between 2000 and 2019. These literatures included 6301 patients with pathologically proven IPMN. Malignancy was defined as high-grade dysplasia and invasive carcinoma. It was significantly associated with symptoms (odds ratio [OR] 1.35, confidence interval [CI] 1.01–1.79), size ≥ 3 cm (OR 1.90, CI 1.51–2.40), cystic wall thickening (OR 2.53, CI 1.50–4.27), mural nodule (OR 4.10, CI 3.38–4.97), main pancreatic duct dilatation (OR 2.98, CI 2.11–4.21), abrupt caliber change of the pancreatic duct (OR 7.41, CI 2.49–22.06), lymphadenopathy (OR 8.55, CI 3.25–22.51), elevated carbohydrate antigen 19-9 (OR 4.01, CI 2.55–6.28), and elevated carcinoembryonic antigen (OR 2.04, CI 1.60–2.61). Multilocular cysts and multiple cysts did not show a significant association with malignancy. This study examined the clinical, radiological, and biochemical features of BD-IPMN, often used as malignancy predictors according to the widely used guidelines. The results confirmed that all the features currently being used are valid.