No charges were brought at the time following an investigation by the Royal Ulster Constabulary.
However, the decision has now been taken to prosecute Soldier A, now 67, and Soldier C, 65, who are surviving members of the Parachute Regiment patrol which fired on Mr McCann.
The Historical Enquiries Team was set up to look into unresolved killings in Northern Ireland and carried out an investigation into Mr McCann's death in 2012.
The case was referred to the Director of Public Prosecutions in Northern Ireland by the attorney general in March 2014, and has been under review since then.
The PPS said: "The decision was reached following an objective and impartial application of the test for prosecution that was conducted in accordance with the code for prosecutors and with the benefit of advice from senior counsel."
The pair are likely to appear in court next year.
A third member of the unit who fired at Mr McCann has since died, the PPS said.
Mr McCann's case is thought to be the second military prosecution involving Northern Ireland since the 1990s.
Files on the 1972 Bloody Sunday shootings by soldiers in Derry/Londonderry are with prosecutors.