Robert Hur, a former senior justice department official during the Trump presidency, will lead the investigation.
Classified files were recently found in Mr Biden’s home and at an office he used after his term as vice-president.
The White House said Mr Biden will fully cooperate with the investigation.
The discovery of the documents have been called a political embarrassment for Mr Biden, as it comes during an ongoing investigation into former President Donald Trump’s own alleged mishandling of classified files.
The first batch of files were found on 2 November at the Penn Biden Center, a think-tank launched by Mr Biden in Washington DC. They were then handed over to the US National Archives, Mr Biden had said.
Mr Garland said a second batch of files were located on 20 December at Mr Biden’s home in Wilmington, Delaware. He added that on Thursday morning, Mr Biden’s lawyers called investigators to notify them of an additional document, also found at the president’s private home.
After an initial probe by US Attorney John Lausch, Mr Garland said his office decided that a special counsel was needed to investigate Mr Biden’s handling of the files due to the “extraordinary circumstances” of the matter.
“This appointment underscores for the public the department’s commitment to both independence and accountability in particularly sensitive matters, and to making decisions undisputedly guided only by the facts and the law,” Mr Garland said.
In a statement, Mr Hur said he will investigate the issue “with fair, impartial and dispassionate judgement”.
White House lawyer Richard Sauber said Mr Biden has cooperated fully with the Department of Justice’s review, and will continue to do so with the special counsel’s probe.
“We are confident that a thorough review will show that these documents were inadvertently misplaced, and the President and his lawyers acted promptly upon discovery of this mistake,” he said.
Sources familiar with the case who spoke with CBS, the BBC’s US partner, said the justice department review included interviews with multiple witnesses who may have knowledge of how the classified documents were handled.
Speaking to reporters on Thursday morning, Mr Biden said that his lawyers immediately notified officials when the first batch of files were discovered in November.
Mr Biden added the additional documents found were locked in a garage next to his 1960s Chevrolet Corvette sports car, “not sitting out in the street”.
“People know I take classified material seriously,” he said.
Mr Biden said his lawyers reviewed other places where documents were stored from his time as vice-president, between 2009 and 2017, after the first files were found, and that review was completed on Wednesday evening.
“The lawyers arranged for the Department of Justice to take possession of the documents,” he said.
Mr Sauber said in a statement that the additional search uncovered “among personal and political papers a small number of additional Obama-Biden Administration records with classified markings”.
All but one of the documents were found in a storage space inside the garage of Mr Biden’s Wilmington, Delaware home, he said.
“One document consisting of one page was discovered among stored materials in an adjacent room,” Mr Sauber added. Lawyers also searched Mr Biden’s Rehoboth Beach home, but found no additional files.
The first batch of files were found in a storage closet at the University of Pennsylvania’s Biden Center for Diplomacy and Global Engagement by Mr Biden’s personal lawyers as they were moving out of the space. They reportedly included intelligence information about Ukraine, Iran and the UK.
Mr Biden is now facing questions about whether the newly discovered files hold sensitive information that could have jeopardised matters of US national security.
Republican Speaker of the US House of Representatives Kevin McCarthy also raised concerns about the timing of the discovery being made public.
“They knew this had happened to President Biden before the (US midterm) election, but they kept it a secret from the American public,” Mr McCarthy said.
Mr Trump is currently under investigation by the justice department after more than 325 classified files – including some marked with Secret and Top Secret designations – were discovered over last year at his Mar-a-Lago estate in Florida.
Investigators said they are looking at whether Mr Trump violated federal law by obstructing the document recovery process or destroying government materials. The former president has denied any wrongdoing.