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Background Despite vaccination and booster shots proving more effective than workplace measures in controlling the COVID-19 pandemic, hesitancy towards compulsory booster shots remains. This study aimed to evaluate the effectiveness of an enhanced educational intervention program in improving the acceptance of COVID-19 booster shots and reducing breakthrough infections among non-healthcare workers in Hong Kong.Methods In this 9-month randomized controlled trial (RCT), workers were randomly allocated to either the intervention or control group. The intervention group received educational sessions at baseline and at 3- month, covering general health and evidence-based information on the efficacy and safety of COVID-19 vaccines and booster shots. The control group received only general health information. All participants were followed up for an additional 6 months. The primary outcomes were intention and acceptance of booster shots, as well as breakthrough infections. The DASS-21 scale was used to evaluate participants’ mental health status, and two-way mixed ANOVA to analyze the group effect. A difference of ≥ 5% in booster uptake between the intervention and control group indicated a practical significance in infection control.Results Among 310 consenting workers, 282 (91.0%) of them completed the trial. At recruitment, the booster uptake rate was similar between the intervention and control groups (62.0% vs. 62.1%). After the educational intervention sessions, the intervention group showed a higher booster uptake rate (76.1% vs. 67.9%). A lower rate of breakthrough infection was observed in the intervention group during the latest follow-up period (23.2% vs. 29.5%); however, no change in the intention to get booster shots were recorded for all subjects.Conclusion This enhanced educational intervention program significantly improves booster uptake rates and reduces COVID-19 breakthrough infection rates among non-healthcare workers. (Trial registration: ClinicalTrials.gov - NCT05197673). (Funding: HMRF Ref.: COVID190104, COVID1903008, and 18190471).