The objective of this meta-analysis was to evaluate the effect of prostaglandin analogues (PGA) on central corneal thickness (CCT) in patients with glaucoma. Key electronic databases were searched for randomized controlled trials (RCTs) involving the CCT effects of prostaglandin use for glaucoma. Primary outcome measures were the mean difference in the CCT measurement from baseline to the last available assessment. Intraocular pressure and other corneal changes were recorded as secondary. Efficacy estimates were measured by their weighted mean difference (WMD) with 95% confidence intervals (CI’s) by using the random-effects model for primary and secondary outcomes Trial sequential analysis was used to determine if the current evidence was sufficient and conclusive. Eight RCTs met our inclusion criteria. A total of 879 patients were included. The overall effect showed that PGA’s had a significant CCT lowering effect (WMD = −7.04, 95%CI: −10.07 to −4.00,
P
< 0.00001). We pooled results of 5 RCT’s on Travoprost (WMD = −10.44, 95%CI: −16.80 to −4.08,
P
= 0.001), seven trials on Latanoprost (WMD = −4.73, 95% CI: −9.70 to 0.25,
P
= 0.06), and three trials on Bimatoprost (WMD = −11.88, 95%CI: −21.03 to −2.73,
P
= 0.01). The WMD across groups in >6 months of PGA use was −11.37 (95%CI: −17.17 to −5.58,
P
= 0.0001), and in <6 months of PGAs group was −8.35 (95% CI: −12.01 to −4.69,
P
< 0.00001), suggesting a longitudinal effect of PGAs on CCT. In conclusion, Bimatoprost and Travoprost caused a statistically significant reduction in the thickness of central cornea. Though only a few studies were included, the narrow confidence intervals and adequate sample size suggest that these findings are valid.