The Department of Health said a student nurse who administered the shot was from an outreach team sent by the New Town Integrated Medical Centre to Tin Shui Wai Government Primary School.
The department added that preliminary findings showed the student nurse injected the syringe before realising that no vaccine was withdrawn from the vial.
The school reportedly arranged two vaccination sessions on campus in March and April, but it’s unclear when the incident happened.
The department said the pupil’s parents were notified immediately and agreed to have another nurse administer a jab.
Officials added that the medical centre followed up on the pupil’s health condition and reported no abnormality.
Authorities said they have asked the medical centre to submit a report on the incident.
The same centre was embroiled in another Covid vaccine blunder in January when it gave dozens of people doses which were past their use-by date.