The former Scrubs star will play an old CIA mentor of Michael Westen (Jeffrey Donovan), reports The Huffington Post.
His character Tom Card will team up with Westen once more and will use his influence at the CIA to help his former protege.
McGinley - who will first appear in the second episode of Burn Notice season six - is known for playing Dr. Perry Cox on Scrubs.
His film credits include 1986's Platoon, 1987's Wall Street and the forthcoming Alex Cross.
Taryn Manning (Sons of Anarchy) will also appear in the new season of Burn Notice as the tough Nicole, a prison inmate who interacts with Fiona (Gabrielle Anwar).
In addition, Anthony Ruivivar (Third Watch) has been cast as Mexican drug kingpin Montero.
The episode will be directed by series star Donovan, who previously directed both 2010 Burn Notice episode 'Made Man' and prequel movie 'The Fall of Sam Axe'.
> Burn Notice Gabrielle Anwar Q&A: 'I want to explore Fiona's past'
Watch a trailer for the sixth season of Burn Notice below: