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"I must admit it came as a bit of a surprise," the 45-year-old Brannigan told Queens' website.
"But it's a new challenge and I'm looking forward to it."
Dundee had sacked Jocky Scott despite the veteran's side leading Division One and remaining strong favourites for the title and promotion.
But Saturday's 3-0 defeat away to bottom side Airdrie United meant that the Tayside outfit had not won in four games, during which their lead has been reduced to three points.
The parting was an amicable one. Kenny Brannigan will now take over the managerial role at Palmerston until the end of the season
Queens have themselves suffered three straight defeats and Brannigan will look to end that run and revive his side's own promotion hopes on Tuesday - at Dens Park against Chisholm's new charges.
"It came as a shock, but the players will be well up for it," Brannigan said of the upheaval at Palmerston and the quick meeting with his club's former manager.
"With Dundee the opposition, the players will be self-motivated and well up for it, so I'm looking for a positive response as it's a big occasion for us all.
"We need to get back on track again after those three defeats and it would be great to get a result at Dens Park."
Brannigan - a central defender who played for 14 senior clubs, including Falkirk, Kilmarnock and Sheffield Wednesday - had previous managerial experience with Clydebank and Queen's Park before becoming Chisholm's assistant in 2007.
Dundee, 10 points above Queens but having played two more games, had turned to Chisholm after having initially held talks with Partick Thistle's Ian McCall.
Queens chairman David Rae showed no bitterness at the departure of his manager, who had been touted for several jobs with Scottish Premier League clubs in recent months.
"Following a phone call from Dundee chairman Bob Brannan this morning, I gave him permission to speak to our manager, Gordon Chisholm, regarding the managerial vacancy at Dens Park," Rae said on Sunday.
"Since then, Gordon has accepted the job and is now the new manager at Dens Park.
"He will take over with immediate effect, but the parting was an amicable one.
"Kenny Brannigan will now take over the managerial role at Palmerston until the end of the season."
Source: BBC Sport
Image - Courtesy of www.qosfc.com
Source: BBC Sport