Background The efficacy of partial nephrectomy (PN) for T1b renal cell carcinoma (RCC) is controversial. The oncological outcomes, the change in postoperative renal function and the perioperative complications are unclear. Methods We searched PUBMED, EMBASE and the Cochrane Central Register for studies from March 1998 to March 2018 for studies comparing PN to radical nephrectomy (RN) for the treatment of T1b RCC. After data extraction and quality assessment, we used RevMan 5.2 to pool the data. Then, we used Stata 12.0 to perform sensitivity analyses and meta-regression. We used the GRADE profiler to evaluate the evidence according to the GRADE approach. Results A total of 16 studies involving 33,117 patients were included in our meta-analysis. No significant difference was found in the 5-year overall survival (OS), 10-year OS, 5-year recurrence-free survival (RFS) and 10-year RFS. The 5-year cancer-special survival (CSS) and 10-year CSS were better in RN compared to PN, respectively, at RR = 1.02, P < 0.05 and RR = 1.04, P < 0.05. PN was better than RN in the preservation of renal function (WMD = -9.15, 95% CI: − 10.30 to − 7.99, P < 0.05). The confidence level grading of the evidence was moderate for 5-year OS, 10-year OS, 5-year CSS, 10-year CSS, 5-year RFS, 10-year RFS, tumor recurrence, decline in eGFR, and postoperative complications. Conclusions PN may provide comparable outcomes in terms of RFS & OS, and better renal function preservation although CSS was worse. Electronic supplementary material The online version of this article (10.1186/s12894-019-0480-6) contains supplementary material, which is available to authorized users.