Launching an advertising van in Aberdeen ahead of the December 12 general election, Scottish Tory leader Jackson Carlaw said he does not support such a tie-up.
He said the Brexit Party will not be able to stop a second referendum on Scottish independence, which is the driving force behind the Scottish Tories' campaign.
Mr Carlaw was speaking hours after Brexit Party leader Nigel Farage offered Prime Minister Boris Johnson the chance of an electoral alliance between the two parties.
Mr Carlaw said: "I just think politics in Scotland are different.
"Because Nicola Sturgeon is making independence the central issue of this campaign, that's not something the Brexit Party can do anything to stop.
"You need to elect a strong Conservative government, with Conservatives from Scotland part of it.
"If you want to stop that second Scottish independence referendum, the Brexit Party aren't going to be able to do that, only the Conservatives can do that.
"That's who people have to support to tell Nicola Sturgeon and make her think again."
Mr Carlaw also said he would not be in favour of his party entering into an alliance with any opposition parties.
He said: "I think they're very often difficult to manage, the important thing is to stand up and say what you believe.
"In this election campaign, we're clear what that is - stop a second independence referendum, get Brexit sorted and let's get the country moving on."
Aberdeen South Tory MP Ross Thomson agreed with Mr Carlaw, saying it is important for parties to "stand on their own" in election campaigns.
He said: "I don't believe in doing deals. I know that Jeremy Corbyn is looking at one with Nicola Sturgeon on the basis of allowing a second independence referendum.
"I think parties need to stand on their own records and their own merits and make sure they're not doing anything where they could sometimes take away choice from voters."
At his campaign launch, Mr Farage said his party would fight every seat in the UK, but would consider stepping back from safe Conservative seats if the Government agreed to abandon its Brexit deal and form a "Leave Alliance".