It is the biggest personal bankruptcy in Irish history.
Mr Quinn said he brought the application north of the border because he was born, reared and worked all his life in Co Fermanagh.
But by declaring himself bankrupt in Northern Ireland, it also means he only has to wait a year before going back into business - rather than 12 years in the Republic.
In a statement, Mr Quinn says he had been left with "no alternative" other than to go bankrupt.
He made heavy losses after he invested in complex share investments at the nationalised Anglo-Irish and said this was one of his biggest errors.
At his financial peak, the 65-year-old was estimated to be worth €4.5bn.
It's the biggest personal bankruptcy in Irish history - Anglo Irish Bank insists he owes them in excess of €2bn.
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In April, Mr Quinn lost control of his manufacturing and insurance business empire after Anglo-Irish Bank struck a deal for the Quinn Group to be transferred to receivership of accountancy firm, KPMG.
He had been plunged into financial trouble by purchasing bank shares which then became worthless.
As part of the deal, all 2,600 manufacturing jobs at the Quinn Group were secured - that includes 1,000 positions in Northern Ireland. At the time, their former boss praised his employees.
Mr Quinn accepts that he owes about €194m to Anglo for property loans which he cannot repay.
But the rest of the alleged debt, which relates to Contracts for Difference (CFDs) used to buy bank shares, is disputed.
The Quinn family are currently suing Anglo, claiming the CFDs were tainted with illegality.
Mr Quinn applied for voluntary bankruptcy through his lawyer and licensed insolvency practitioner, John Gordon of Napier and Sons.
The order was granted during a brief hearing before a Master at the High Court in Belfast.
Following confirmation, Mr Quinn said: "I have done absolutely everything in my power to avoid taking this drastic decision.
"The vast majority of debt that Anglo maintains is owed is strenuously disputed. I cannot, however, now pay those loans which are due."
The businessman said he had "worked tirelessly" to find a solution to the problems.
"Anglo, and more recently the Irish Government, are intent on making scapegoats of my family and I," he claimed.
According to Mr Quinn, the bank has attempted to avoid acknowledging "a lack of corporate responsibility, self-interest and lack of regulation that prevailed at the time".
His allegations are now the subject of High Court proceedings.
Following Anglo taking control of the Quinn Group of companies, which I and a loyal team spent a lifetime building, I find myself left with no alternative.
Sean Quinn
Mr Quinn accepted: "I am certainly not without blame. I am not in the business of pointing fingers or making excuses.
"However, recent history has shown that I - like thousands of others in Ireland - incorrectly relied upon the persons who guided Anglo and who wrongfully sought to portray a 'blue chip' Irish banking stock."
He said that he and his team had developed one of the most successful businesses in Irish history, with the group generating more than 5,000 jobs and contributing in excess of €1bn in tax revenues.
Mr Quinn rejected any suggestion that he had brought down the empire, adding that prior to Anglo's takeover, it was a profitable business paying all interest on 100% of its debts as well as having enough surpluses to develop further.
He also claimed: "Anglo has supported and promoted an ill-conceived and highly damaging receivership programme which I believe, if it continues on its current road, is destined for certain and catastrophic failure."
The statement added: "My family and I have been subjected to relentless negative media coverage over the past three years.
"I have been portrayed as a reckless gambler who bet on a bank. I have never sought publicity, nor have I courted the media. On the contrary I have developed a reputation for avoiding the media glare.
"Sadly this now seems to have worked very much to my disadvantage, especially when compared with the sophisticated and massively expensive publicity campaign operated for and on behalf of Anglo."
Solicitor and Insolvency Practitioner John Gordon said Mr Quinn was now a man of modest means.
"He has been left with very little, with very minimal assets."
"Apart from drawing a pension he has no other visible means of income."
"He is in relatively poor circumstances because the Quinn Group stopped paying him any salary in July of this year."