The 65-year-old will appear in Belfast Magistrates Court on Monday to be charged with the murders of John Devine in 1989 and John O'Hara in 1991.
John Devine, 37, was shot dead at his home on Fallswater Street in west Belfast on 23 July 1989.
He was sitting in his living room with his 13-year-old son when three men forced their way in and shot him.
John O'Hara, 41, was murdered on Dunluce Avenue in south Belfast on 17 April 1991.
He was working as a taxi driver and had gone to pick up a passenger at 22:15 BST, when he was approached by two masked men who fired several shots at the car, fatally injuring him.
Officers from the Legacy Investigation Branch (LIB) of the PSNI arrested Mr Rea on Tuesday.
Last September the LIB announced that it would re-examine the murders after they gained access to tapes containing interviews Mr Rea gave to the Boston College 'Belfast Project'.
Belfast loyalist Winston 'Winkie' Rea has been charged with two counts of murder dating back more than 20 years.