David Coburn said Ukip would back a referendum on Scotland returning to the Union as part of the next General Election campaign.
He also revealed plans to help make Scotland Tory-free by targeting Conservative David Mundell's seat.
Ukip made its electoral breakthrough north of the Border last week. The SNP, which made opposing Ukip a key plank of its campaign, was denied a third MEP.
Coburn, who has made a series of controversial remarks about drugs, the birth rate and gay marriage, has now caused a row about the referendum.
A cross-party consensus has so far existed on how to react to September's result: the SNP has said a No vote would kill independence for a "generation", while the pro-Union parties have agreed to accept a Yes victory.
But asked how he would respond as an MEP for Scotland to a Yes vote, Coburn said: "I would want Scotland returning to the UK and I would be pushing for renegotiation."
He said post-referendum horse-trading would mean a bad deal for Scotland and the rest of the UK, noting: "We would use the next General Election to call for another referendum. I think we could get support from Labour on this."
He added: "Hopefully the English will have us back, but I fear they won't."
Coburn's remarks confirm that any post-Yes negotiations with the UK Government will be a key issue at the General Election.
Mundell's Dumfriesshire, Clydesdale and Tweeddale seat will also feature prominently in Ukip's election strategy.
The Tory minister held the seat in 2010 with a 4194 majority over Labour. Coburn said Ukip will mount a challenge in the hope of unseating the moderate Tory.
He said: "I don't think he would be a great loss. We think we can do well there."
SNP MEP Ian Hudghton said: "Ukip are a big embarrassment to the No campaign. The idea that they would look to ignore the democratic decision of the people of Scotland is absolutely ridiculous and shows exactly why it is so dangerous for the Westminster parties to … pander to Ukip after their win south of the Border."