Sir Tim, who was awarded the Nobel prize in physiology or medicine in 2001, made his remarks at the World Conference of Science Journalists in South Korea.
The 72-year-old said: "Let me tell you about my trouble with girls. Three things happen when they are in the lab: you fall in love with them, they fall in love with you, and when you criticise them they cry."
Sir Tim Hunt has resigned from UCL
The comments prompted outrage from both within and outside the science community and though Sir Tim later attempted an apology of sorts, as of Thursday the honorary professor had resigned from University College London Faculty of Life Sciences.
Hopkins, who had appeared on LBC Radio to defend Sir Tim tweeted her dismay, drawing parallels between Sir Tim’s voluntary resignation and the beheadings and torture carried out by the Islamic extremist group ISIS.
She said: “Sir Tim Hunt resigns from UCL. Bloody hell. Public shaming has reached in proportions. ISIS in another guise. ‘Conform or get out’.
Speaking to John Stapleton on LBC, Hopkins said that his comments were "not that outrageous" and that too many limits are placed on people's free speech.
When asked why she was defending Sir Tim, Hopkins said: "Sir Tim Hunt is a great guy. He's a funny guy. He has a dry British wit.
Katie Hopkins has likened the 'public shaming' of Sir Tim to the behaviour of Islamic extremist group ISIS
"Now if you take a load of scientists, specifically South Korean scientists who have got about as much sense of humour as my mother in law and she's dead, then you are not really going to get much of a laugh back.
"But actually if you read behind those words and you stop flapping your bingo wings and moaning just because you're a girl, you will find that actually he was being quite truthful.
"His point about falling in love not being terribly helpful is because he thinks that it creates an imbalance, and unequal playing field and it disrupts the science."