In 1991, following Service in the KGB Border Troops from 1985–87, Borodin graduated in International Economics and Finance from the International Economics Department at the Moscow Finance Institute. From 1989 to 1990 he was a visiting student at the University of Passau, Germany. He worked for Dresdner Bank in Germany - which has deep ties to former members of the KGB and Stasi services - on an 18-month training course in Dortmund. He then moved to Frankfurt to work at the bank’s head office in the Financial Institutions Department. He left Dresdner Bank in late 1993 and in March 1994 started working for the Government of Moscow as an economics and Finance adviser to the Mayor of Moscow, Yury Luzhkov.

What became one of the biggest players in Russian banking began as a six-person operation founded in 1995 by the Moscow City Government, which originally held a 51% stake. Under the political patronage of Luzhkov and the leadership of Borodin it weathered the crisis of 1998 and subsequently grew rapidly from a local bank largely serving the City Government to a national bank with a greatly enlarged client base and offering a broad range of services. The bank became increasingly independent of the City Government, which in 2008 reduced its stake to 46.6%, with a corresponding reduction in the number of bank-appointed Directors. As the bank expanded, Borodin and his ally Lev Alaluev purchased significant stakes of their own – more than 20.32%. There was no evidence on how Borodin and Alaluev got the necessary funding for such a big purchase.(in Russian)

In December 2010, before the sale of the City Government's stake took place, the Audit Chamber of the Russian Federation announced that it had launched an audit of Bank of Moscow at Sobyanin's request. The investigation revealed a loan provided by the bank to Premier Estate Company.

In July 2011 it was announced that Bank of Moscow would receive a US$14 billion bail-out from the Russian state.

In August 2012 Borodin bought Park Place, Britain’s most expensive house, near Henley-on-Thames, and paid £140 million ($219 million) for it.

Speaking to Vedomosti newspaper on 1 March 2013, he said he had been granted political asylum in the UK "a few days ago" after his lawyers submitted a request. He also accused Russian Prime Minister Dmitry Medvedev, who was the country's President when the Criminal case was launched, of being the "chief initiator of all this persecution and hounding".

On 13 May 2015 it was reported that a Russian Court had ordered the seizure of Andrei Borodin's Park Place mansion in Henley-on-Thames.

Borodin has contested the legality of this on a number of grounds, including that competitive tender ought to have been used to maximise the share price. None of the protests were found correct or justified by court. Borodin and his allies were dismissed and VTB's Chairman Andrey Kostin and first deputy Mikhail Kuzovlev became the Bank’s Chairman of the Board of Directors and President respectively.