Predicting the aggressiveness of solid pseudopapillary neoplasms (SPNs) remains an important goal. The present study aimed to identify perioperative factors that can predict patients who will develop clinically aggressive SPN. Records of individuals with pathologically confirmed SPN from 2006 to 2017 were obtained from the patient registry database of Yonsei University, Severance Hospital. For this study, aggressive behavior was defined as SPN that had recurred, metastasized, or involved adjacent organs. A total of 98 patients diagnosed with SPNs were analyzed retrospectively. Of these, 10 were reported to have SPNs with aggressive characteristics. We found that age (≥40 years; p = 0.039), symptomatic presentation (p = 0.001), tumor size (>10 cm; p < 0.001), positron emission tomography/computed tomography (PET/CT) classification (p < 0.001), and lymphovascular invasion (p = 0.003) were significantly correlated with aggressive behavior of SPNs. Multivariate analysis showed that PET/CT configuration (p = 0.002) (exp(β)111.353 (95% confidence interval (CI): 5.960–2081), age ≥40 years (p = 0.015) (exp(β) 23.242 (95% CI: 1.854–291.4)), and lymphovascular invasion (p = 0.021) (exp(β) 22.511 (95% CI: 1.595–317.6)) were the only independent factors associated with aggressive SPN. Our data suggest that age ≥40 years, PET/CT Type III configuration, and lymphovascular invasion are independent factors associated with aggressive SPN. This information can help clinicians develop individualized management and surveillance plans to manage patients more effectively.