Background and Objective: Health literacy (HL) is an important determinant of health outcomes, as it determines individuals’ abilities to process and use health-related information. However, the association between HL and vaccine delay remains unclear. This study aimed to assess how HL affected the delayed COVID-19 vaccination among Hong Kong adults. Methods: A cross-sectional study using Quota sampling was conducted. Self-administrated online questionnaires were distributed to a web panel. Multivariable logistic regression models were used to explore associations among three domains (i.e., functional, interactive, and critical) of HL and vaccine delay while adjusting for social demographic and health-related characteristics. Sensitivity analyses were performed to ensure the robustness of the Results. Results: A total of 401 participants were recruited between August to September 2022. Over half (52%) of the participants have inadequate HL. The proportion of participants with delayed first and third doses of COVID-19 vaccination is 30.9% and 28.2%, respectively. In multivariable analysis, the risk of delaying the first dose was higher among participants with inadequate functional HL (OR = 0.58, p = 0.015) and adequate levels of two subdomains of critical HL (OR = 1.82, p = 0.013; OR = 1.91, p < 0.01). Participants who delayed their third doses were likely to have inadequate interactive HL (OR = 0.52, p = 0.014) and an adequate level of one subdomain of critical HL (OR = 1.71, p = 0.039). The sensitivity analyses confirmed these findings. Conclusions: Functional and interactive HL were positively associated with COVID-19 vaccination. However, a negative association between critical HL and vaccination was reported. These findings indicate a challenge for health partitioners to promote vaccination campaigns to the public, especially those with low functional and interactive HL and high critical HL. Researchers and policymakers may need to monitor and report HL when they study vaccination decision behaviours.