Background: Intraocular pressure (IOP) measurement should be accurate in a paediatric population with primary congenital glaucoma (PCG).Aim: This study aims to investigate the difference between the change in IOP measurements using rebound tonometry (RBT) and handheld applanation tonometry (AT) (Perkins applanation tonometer [PAT]) in patients with and without PCG.Setting: Johannesburg, South Africa.Methods: Measurements were taken under anaesthesia, using RBT and AT at 0 min, 5 min and 10 mins after induction and prior to intubation. Corneal pachymetry and corneal diameters were measured.Results: Sixty-five children were included, 19 with PCG and 46 without PCG. The mean age (standard deviation [s.d.]) was 3.2 (2.25) years and 4.8 (2.4) years, respectively. The overall mean difference in IOP between RBT and PAT across both PCG and non-PCG groups was found to be 4.92 mmHg (95% confidence interval [CI]: 2.80 – 7.03) p 0.001, with RBT having higher readings. This difference was greater in the PCG group, with the IOP difference of 9.05 mmHg (95% CI: 2.6 – 15.5) p = 0.004. Mean corneal pachymetry (s.d.) was 585.6 (81.48) µm in the PCG group and 518.31 (39.9) µm in the non-PCG group. Univariate analysis showed that IOP was significantly related to corneal pachymetry, with a 11 mmHg increase in IOP for every 100 μm change in corneal thickness for measurements done with RBT (p 0.001), compared to 4 mmHg using PAT (p = 0.008).Conclusion: Intraocular pressure measurements done with RBT in children with and without PCG were overestimated compared to PAT.Contribution: This difference was more pronounced in PCG patients. In addition, IOP was significantly related to corneal thickness.