AIM: To evaluate the overall endophthalmitis incidence and the effectiveness of potential prophylaxis measures following phacoemulsification cataract surgery (PCS). METHODS: The PubMed and Web of Science databases were searched from inception to April 30th, 2021. We included studies that reported on the incidence of endophthalmitis following PCS. The quality of the included studies was critically evaluated with the Newcastle-Ottawa quality assessment scale. The random effect or the fixed-effects model was used to evaluated the pooled incidence based on the heterogeneity. The publication bias was assessed by Egger's linear regression and Begg's rank correlation tests. RESULTS: A total of 39 studies containing 5 878 114 eyes were included and critically appraised in the Meta-analysis. For overall incidence of endophthalmitis after PCS, the Meta-analysis yielded a pooled estimate of 0.092% (95%CI: 0.083%-0.101%). The incidence appeared to decrease with time (before 2000: 0.097%, 95%CI: 0.060%-0.135%; 2000 to 2010: 0.089%, 95%CI: 0.076%-0.101%; after 2010: 0.063%, 95%CI: 0.050%-0.077%). Compared with typical povidone-iodine solution (0.178%, 95%CI: 0.071%-0.285%) and antibiotics subconjunctival injections (0.047%, 95%CI: 0.001%-0.095%), the use of intracameral antibiotics significantly reduced the incidence of endophthalmitis after PCS (0.045%, 95%CI: 0.034%-0.055%, RR: 7.942, 95%CI: 4.510-13.985). CONCLUSION: Due to the advancement of phacoemulsification technology and the widespread use of intracameral antibiotics, the incidence of endophthalmitis following PCS shows a decreasing trend over time. The use of intracameral antibiotics administration will significantly reduce the risk of endophthalmitis.