Mr Nuttall described it as "a great honour and a privilege" to be standing for Ukip in the seat.
The Lincolnshire town of Boston had the highest majority of Brexit voters in the June referendum with more than 75 per cent voting to leave the EU.
The seat, where Ukip came second in the last election, is currently held by the Conservatives' Matt Warman, a Remain backer, with a majority of 4,336.
Mr Nuttall, who unsucessfully stood in the Stoke-on-Trent Central by-election earlier this year, said: "The constituency voted overwhelmingly for Leave inspired in part by the massive betrayal of our fishing industry by successive Governments, something that today's Conservative Party led by Theresa May looks set to repeat.
"I will make it my mission to stand up for the people of Boston and Skegness and ensure there is no backsliding on Brexit."
Sue Blackburn, chairman of the Ukip Boston and Skegness branch, said: "As branch chairman, I would like to say on behalf of the Boston and Skegness branch how delighted we are to have our leader standing in this election and Paul will have the upmost support of this branch."
Mr Nuttall had kept people guessing about where he would stand for Parliament after confirming he would put himself forward as a candidate during an interview with LBC on Thursday.
Asked why he was standing in Boston and Skegness, Mr Nuttall said: "Because we have a great opportunity there. We've got councillors right across the constituency. It voted to leave the European Union by 70 per cent to 30 per cent.
"I think we've got a great chance of running an active campaign and the branch was very keen that I stood in that area."
Asked why he revealed he was standing during an event 165 miles away in Hartlepool, he said: "I never said I was standing in Hartlepool. I was always coming here today. It's been in the diary for weeks.
"I want to get there now and campaign alongside our local activists because we believe we have a great chance in Hartlepool. We only need a 4 per cent swing to take the seat off Labour."
Asked if he can win in Boston, he said: "Who knows? There's six weeks to go in this campaign, the Conservative MP campaigned to remain during the referendum, 70 per cent of people voted to leave the European Union and we've got a good active branch. We'll be giving it a good go."
Mr Nuttall skipped a planned mini-rally with supporters outside a Hartlepool pub after a confrontation between local residents and anti-Ukip protesters turned into a fight in front of the venue.
He moved to another Hartlepool pub to conduct media interviews before beginning campaigning.
Activists had to be pulled from the Marriott County Hall hotel by security guards after two separate groups broke in and began chanting about “Islamophobia”.
Mr Nuttall was due to officially launch UKIP’s manifesto but had to delay his speech due to the commotion, caught on camera and film by the assembled press.
After the event, when asked which seat he would be standing in for the election, he told reporters they would need their "bucket and spade".