Controversial figure McQuaid is aiming for a third term in office when elections take place in September.
The Swiss federation's endorsement has rescued McQuaid from a potentially embarrassing snub.
Traditionally a candidate is supported by his own country's federation.
His candidacy had already been endorsed by the Irish Federation in April by a vote of five to one but board member Anthony Moran, who had voted against McQuaid, subsequently resigned, leading to Cycling Ireland calling an extraordinary general meeting.
That threw up the prospect of the Irish federation withdrawing their backing.
But having moved to Switzerland in 2005 when first elected UCI president, McQuaid qualified for Swiss backing.
"I am delighted that the board of Swiss Cycling has endorsed my nomination," said McQuaid in a statement released by the UCI, which is based in Aigle in the canton of Vaud.
"It has become clear that my nomination in Ireland has been politicised by a small group of people."
McQuaid has come under fire over the Lance Armstrong doping scandal amid allegations he was complicit in a cover-up of failed tests taken by the American.
The Irishman insists that it is only due to his organisation catching Tyler Hamilton and Floyd Landis that the pair blew the whistle on Armstrong's own doping with the US Postal team.