Aim: Owing to the limited ability of current imaging modalities, several clinical T1 renal cell carcinomas (cT1 RCCa) can be pathologically upstaged to T3a (pT3a) after surgery. There have been some controversies regarding the oncological safety of partial nephrectomy (PNx) compared with radical nephrectomy (RNx) in these patients. We compared oncological outcomes of PNx and RNx in patients with upstaged pT3a RCCa. Methods: A systematic review was performed following the PRISMA guideline. PubMed, MEDLINE, Embase were searched. Oncological outcomes [recurrence-free survival (RFS), overall survival (OS) and cancer-specific survival (CSS)] between PNx and RNx were compared. The GRADE approach was used to rate the certainty of evidence. Results: A total of 7406 patients in 12 articles related to upstaged pT3a RCCa were included. In adjusted analysis, no difference was observed in RFS [hazard ratios (HR) 0.87; 95% confidence intervals (CI), 0.57–0.95; p = 0.88] and CSS (HR, 0.78; 95% CI, 0.59–1.04; p = 0.09) for PNx and RNx. Meanwhile, PNx was significantly associated with favorable OS compared with RNx (HR, 0.74; 95% CI, 0.57–0.95; p = 0.02). Conclusions: Our meta-analysis shows that patients treated with PNx have better or at least similar oncological outcomes compared with RNx in patients with upstaged pT3a RCCa from cT1. In particular, patients who had undergone PNx show a significantly improved OS. If PNx is available, we recommend performing PNx for all cT1 RCCa, even in patients with upstaging potential. However, due to the low level of evidence, large-scale randomized trials are required.