Trachoma is the leading infectious cause of blindness worldwide and is targeted for global elimination as a public health problem by 2030. As we approach this target, defining when population-level trachoma control interventions can be stopped, and determining how post-intervention surveillance should be performed, are becoming increasingly important. Molecular diagnosis of ocular Chlamydia trachomatis (Ct) using polymerase chain reaction (PCR) provides a highly sensitive and specific indicator of infection, yet there are currently no programmatic guidelines based on Ct infection. We assembled 86 cross-sectional surveys of ocular Ct infection from 13 countries, representing data from 46,914 children aged 1-5 years. Our analyses suggest that infection prevalence of 0.81% in this age group corresponds to a threshold below which population-level interventions can be stopped with at least 90% confidence. Correspondingly, with confidence exceeding 90%, we propose that interventions should continue when infection prevalence is greater than 1.99%. Interpretation of infection surveillance data is a generalisable challenge in low-prevalence settings for many infectious diseases. This study proposes a robust framework for how Ct infection surveillance could support accurate population-level assessments of trachoma endemicity and could allow a step-change in decision-making precision for programmes as we approach the endgame for trachoma elimination.