Doncaster will take up the role for three-year period from 2013/14 to 2015/16 and will follow in the footsteps of former SPL Chairman Lex Gold who previously served on the board.
The body was founded in 2005 and now has 30 European Leagues as members.
"I feel honoured to be appointed as a director of the EPFL," said Doncaster.
"I am delighted that Scottish football should once again be represented on the board of such an important body.
"The EPFL plays an increasingly central role within European football policy at the highest level - and it is important Scotland is able to contribute effectively to the debate.
"I look forward to representing all 42 clubs of the SPFL within the association of European Professional Football Leagues."