The former NAB boss, who resigned from that job in 2019 after receiving scathing criticism during the banking royal commission, was on Monday announced as the Bombers' successor to Xavier Campbell.
But within hours of his appointment, Thorburn's links to a controversial church organisation were thrust into the spotlight, and by Tuesday evening the embattled Bombers were left searching for their third CEO in less than two months.
Thorburn is chairman of City on a Hill, a church that condemns homosexuality and has an article on its website from 2013 titled 'Surviving Same Sex Attraction as a Christian'.
Essendon president Dave Barham said the board had accepted Thorburn's resignation after they had made it clear he couldn't hold positions at his church and the Bombers.
Barham fronted a hastily-organised press conference at the MCG on Tuesday evening.
"He was upset, really upset," Barham told reporters of Thorburn's reaction.
"He wanted to be CEO of Essendon football club and he was upset.
"In the end, Andrew decided that he would stay with his church and he couldn't be CEO.
"It was about his position as chairman of the board, those views of his church didn't match with our views and values."
In his first, and only, interview after being appointed to lead Essendon, Thorburn had said he understood some of the church's views "are offensive and upset people".
Thorburn joined City on a Hill in 2014 and he says some of the articles and readings on the church's website pre-date his involvement and he had never heard such sentiments expressed during his time there.
Barham stressed both the board and Thorburn had been unaware of the church sermons before reading about them via news outlets.
"At the end of the day, I reference checked Andrew thoroughly," Barham said.
"I rang five incredibly high-profile people who had worked with him, and worked for him.
"I had no reason to think anything other than he was a suitable candidate.
Before leading NAB between 2014 and 2019, Thorburn was in charge of Bank of NZ for six years.
He pointed to those jobs where he led thousands of "diverse" people as evidence he was the right person to take Essendon forward.
"My role as a CEO is to ensure the organisations I lead, which I think my record stands for this, are inclusive and welcoming and caring," Thorburn told SEN on Tuesday.
Victorian premier Daniel Andrews even commented on the situation on Tuesday, labelling the church's views "absolutely appalling" but said he would continue to support Essendon and renew his membership.
Essendon's bungled chief executive process follows a disastrous 2022 season on the field that led to the sacking of coach Ben Rutten with a year to run on his contract.
The Bombers unsuccessfully attempted to lure four-time Hawthorn premiership coach Alastair Clarkson in the week leading up to Rutten's axing.
Clarkson eventually chose to coach North Melbourne but his tenure is now in limbo due to serious historical allegations levelled at him and the Hawks.
Former Kangaroos coach Brad Scott was last week unveiled as Rutten's successor in a major positive for the club.
However, Essendon board member Kevin Sheedy immediately dampened enthusiasm by hitting out at his own club for the decision to choose Scott.
The four-time Bombers premiership mentor said he was "extremely disappointed" while the club said the board's call on Scott was unanimous, with Sheedy opting to vote for James Hird to return as coach instead.
