Purpose: To examine the prevalence and risk factors for hypothalamus–pituitary–adrenal axis suppression (HPA axis suppression) in infants receiving glucocorticoid (GC) eye drops after ocular surgery. Methods: This was a clinical observational cohort study. Children under the age of two receiving GC eye drops after cataract or glaucoma surgery between 1 January 2017 and 31 December 2021 were included at one centre. Medical history and results of the adrenocorticotropic hormone (ACTH) stimulation tests were obtained through patient charts. Results: Forty-nine infants were included in the study. Ten out of 22 patients (45.5%) tested during treatment and two out of 27 patients (7.4%) tested after treatment cessation were diagnosed with HPA axis suppression. The duration of HPA axis suppression extended beyond 3 months in 8 out of 12 patients. Logistic regression showed that infants with HPA axis suppression had received a higher GC dose/body weight/day before the first ACTH test (p < 0.001). There was a 79% (95% CI:1.28;2.50) increase in the odds of having HPA axis suppression for a 0.01 mg GC increase/kg/day corresponding to an additional daily eye drop for an infant weighing 5 kg. There was an association between HPA axis suppression and number of days from surgery to test (p = 0.003), age at surgery (p = 0.035) and cumulated GC dose (p = 0.005). Three infants with HPA axis suppression had affected growth and one had Cushing-like features, but there were no cases of Addisonian crisis. Conclusion: Infants are at risk of having hypothalamus–pituitary–adrenal axis suppression if they receive a high daily glucocorticoid dose per weight by topical ocular administration. Infants receiving glucocorticoids after ocular surgery should be monitored clinically or by ACTH testing.