The teacher was working at Fowlmere Primary School in Cambridgeshire when the incident took place earlier this month.
It is thought that the teacher placed sticky tape over the child's mouth 'as a joke'.
The school said an investigation had been carried out and an apology made to the pupil's parents.
A spokesperson for the school told local newspaper Cambridge News: "Although there was no ill intent or unkindness intended it is clear this incident should not have happened and the member of staff has resigned from their post.
"We have spoken to the child's parents and apologised as this fell below the standards we expect."
Earlier this year another primary school teacher was suspended for allegedly putting sticky tape over the mouths of more than 20 of her 10-year-old pupils after they refused to stop giggling and talking during her art lesson.
One parent told reporters that his daughter was shocked by what had happened and that the tape had hurt her mouth.
"When she removed it at the end of the lesson it took the skin off lips and made her lips bleed," said Rob Lovell.
"She was a bit upset telling us because she thought she'd done something wrong."
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