He subsequently returned to Athens, Greece to coach Olympiacos C.F.P., earning the championship title in 1987. He also coached Aris FC from 1987- 1990 and Levadiakos from 1991-1992. He returned as Head Coach of the Greek National Football team in 1992  and led the team to its first appearance in a World Cup in 1994. He coached Iraklis FC in 1997 and coached Aris Thessaloniki F.C. from 1998- 1999.
Following his retirement from coaching, Panagoulias served as President of Aris Thessaloniki F.C. in 2002. During the 2004 Athens Olympic Games, he served as venue manager for the soccer events held in Athens. His biography, was published in Greece in November 2007.
He was elected member of the city council of Thessaloniki, and was a candidate for the Greek Parliament and a candidate[when?] for the European Parliament representing Greece. He was a FIFA instructor, a National Faculty member of the US Academy of Sports and a member of the USSF Coaches Council.
Panagoulias was a member of the USA Soccer Federation Hall of Fame.