Background: Prostaglandin analogs (PGAs) are first-line antiglaucoma agents that appear to either decrease or increase central cornea thickness (CCT), creating controversy regarding the benefits of PGAs in treating CCT. Purpose: We performed the first meta-analysis of observational studies to evaluate the effects of PGAs on CCT in patients with glaucoma or ocular hypertension (OHT). Methods: This systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement. A literature search was performed of the PubMed, Embase, Cochrane Library, System for Information on Grey Literature in Europe (Open Grey), and ClinicalTrials.gov databases and the references of retrieved studies. Only observational studies were included in the meta-analysis. The final CCT of patients and 95% confidence interval (CI) of each study were extracted. Study quality was assessed using the Newcastle-Ottawa Scale (NOS) and the Agency for Healthcare Research and Quality (AHRQ). A fixed-effects model was used to calculate the weighted mean difference (WMD) and 95% CI. Subgroup analyses based on several stratified factors such as public bias (Begg’s test) and sensitivity analyses were performed. Results: Five cohort, 5 case-control, and three cross-sectional studies including 2,722 subjects were included. The pooled effect of all thirteen studies showed that PGAs reduced the CCT of patients with glaucoma or OHT slightly but significantly (WMD = −9.37; 95% CI [−12.18, −6.57]; p = 0.00; I2 = 45.5%). Significant effects were also observed in all three study designs: cohort (WMD = −5.17; 95% CI [−9.52, −0.82]), case-control (WMD = -15.31; 95% CI [−22.66, −7.97]), and cross-sectional (WMD = −8.65; 95% CI [−17.30, −0.01]). In addition, subgroup analysis of exposure time showed the effect of PGAs to be more obvious in the first (WMD = −5.81; 95% CI [−9.49, −2.14]) and second (WMD = −13.73; 95% CI [−20.19, −7.28]) years. Conclusions: The pooled effects of previously reported studies suggest that PGA use can reduce the CCT of patients with glaucoma or OHT slightly but significantly, with this effect more pronounced in the first 2 years. These findings suggest that clinicians must closely monitor changes in CCT in the first 2 years of PGA use to identify cases of intraocular pressure misestimation and the efficacy of PGAs.