In a statement, Mr Nuttall, the MEP for North-West England, said: “After much soul-searching over the past week, I have concluded that I must, as of today, resign as a member of Ukip.
“I do this with an immense amount of reluctance and regret as I have worked tirelessly for the party for the past fourteen years.
“I am resigning because the party is being taken in a direction which I believe is harmful to Brexit. The association with Tommy Robinson will simply appal many moderate Brexit voters and inevitably be detrimental to the cause.
“The Tommy Robinson issue should have been shelved and debated within the party following Brexit in line with the sensible decision taken by the National Executive Committee last month. The party leadership and my MEP colleagues have been aware of my views on this issue for some time.
“Putting Tommy Robinson front and centre, whilst Brexit is in the process of being betrayed is, in my view, a catastrophic error. To conflate Brexit and Robinson at this crucial moment is to put the Eurosceptic cause in danger and I cannot and will not be party to that.
“I will continue to serve the North West of England in the European Parliament until my term expires.”
Former Ukip leader Nigel Farage confirmed earlier this week he would be leaving membership of the party due to Mr Robinson’s appointment.
Mr Farage had previously called for Ukip leader Gerard Batten to be ousted over the appointment of the English Defence League founder.