Currently, the optimal treatment approach for breast benign intraductal papilloma (IDP) diagnosed via biopsy remains uncertain. There is ongoing debate regarding the feasibility of clinical follow-up and the criteria for selective surgical excision. This study aims to conduct a meta-analysis to determine the rate of upgrade from breast benign IDP and identify predictive factors associated with the conversion of benign IDP to high-risk lesions or carcinoma, which could guide healthcare practitioners in selecting the appropriate clinical treatment strategy. We conducted a comprehensive search across multiple databases (PubMed, Web Of Science, Cochrane Library, and Embase) for studies published between 2012 and 2023 that evaluated upgrade rates and predictive factors of breast benign IDP diagnosed via biopsy. In addition, we included studies that reported on the clinical follow-up of patients with breast benign IDP. In total, 32 studies comprising 7371 cases of biopsy-diagnosed breast benign IDP were included. Among these cases, 720 demonstrated an upgrade to high-risk lesions or carcinoma, resulting in an upgrade rate of 6.94% [95% confidence interval (CI): 3.0-8.0%]. A subgroup of 1713 patients was clinically followed up, demonstrating an average follow-up duration of 30.95 months. Among them, 26 cases experienced an upgrade to high-risk lesions or carcinoma, yielding an upgrade rate of 1.51% (95% CI 0.00-2.00). Furthermore, we identified nine predictive factors associated with the upgrading of breast benign IDP, which included age at diagnosis, personal history of breast cancer, family history of breast cancer, multiple IDPs, lesion size ≥ 10 mm, palpable mass, calcification, and the presence of mass and asymmetry in mammographic findings. Although the conversion rate of breast benign IDP to high-risk lesions or carcinoma is relatively low, timely identification of predictive factors associated with benign IDP upgrades may help selecting the optimal clinical treatment strategy, such as surgery for patients with benign IDP presenting one or more predictive factors, while clinical follow-up for those without specific risk factors.