Christina Wilkinson, head at St Andrew's CE Primary School in Oswaldtwistle, Lancashire, was responding to a blog post by Tom Sherrington about evolution.
Her post, which claimed there was more evidence in support of the Bible, has since been taken down from the account @WilkinsonHead.
It read: "Evolution is not a fact. That's why it's called a theory! There's more evidence that the Bible is true."
In response, Tony Hopkinson (@TonyJHopkinson) tweeted: "Evolution is fact @WilkinsonHead By Natural Selection is the theory. Wilful ignorance is not a useful trait in a teacher."
After a number of abusive and mocking tweets Ms Wilkinson was forced to issue a statement: "I'd like to make it clear that we teach the full national curriculum in school and that our pupils receive a fully rounded education."
She added that the comment had been made using her personal Twitter account, and "represents my own views".
Mr Sherrington said: "The response was largely fuelled by an unfortunate Twitter comment from a Christian primary school teacher who was then battered with over 700 replies in 24 hours before she took her twitter account and school website down."
He added that he had made direct contact with her to offer support.
"She was bemused by the reaction and, whilst she was wrong to pit evolution against the Bible, she didn't deserve the abuse," he said.
