Early coaching career Pagan's coaching career began when he took the role of captain-coach of the
Yarraville Football Club in the VFA second division in 1979. He piloted the team to the 1980 minor premiership and Grand Final, but the club lost the Grand Final against
Brunswick. Pagan then returned to North Melbourne, and had great success as its Under-19s coach over the following decade. Pagan led the team to nine consecutive Under-19s Grand Finals from 1983 to 1991, resulting in five premierships: in 1984, 1987, 1988, 1990 and 1991. After the AFL's Under-19s competition was disbanded at the end of 1991, Pagan was signed by the
Essendon Football Club, where he led its reserves team to the
Victorian State Football League premiership in 1992.
North Melbourne Football Club Pagan returned again to North Melbourne in the
1993 season, and was appointed senior coach. He had an immediate impact at the Kangaroos, taking the side to the finals that year. Pagan led North Melbourne to a premiership in
1996. Pagan also led North Melbourne to the
1998 AFL Grand Final but fell short and lost to
Adelaide. Pagan then led North Melbourne to another premiership in
1999 and reached at least the preliminary final every year from 1994 to 2000. He was known for pioneering a successful tactic which was termed "Pagan's Paddock", based around his key forward
Wayne Carey. The coaching strategy involved moving all forwards out of the
50-metre arc and midfielders bombing the ball into empty space. The key forwards would run with the flight of the ball to take a mark or running goal. Pagan was then replaced by
Dean Laidley as senior coach of North Melbourne.
Carlton Football Club At the end of 2002, Pagan was appointed senior coach of the
Carlton Football Club, replacing
Wayne Brittain, after Brittain was sacked when Carlton under Brittain finished sixteenth (last-on the ladder position) for the
wooden spoon in the
2002 season. Brittain had a year remaining on his contract, and was paid out by the club. Pagan's attempt to rebuild the side was not helped by the fact the club had been hit with
salary cap breaches which prevented the club from rebuilding its playing list in the short term. As a result of these penalties, in Pagan's first season as Carlton Football Club senior coach in the
2003 season, Carlton under Pagan endured another unsuccessful season, finishing fifteenth (second-last) on the ladder with four wins and eighteen losses. However, this proved to be a false dawn, when Carlton under Pagan ended up receiving two consecutive
wooden spoons in the
2005 season with four wins, one draw and seventeen losses, and in the
2006 season with three wins, one draw and eighteen losses. however, it was decided to extend his contract until the end of the 2008 season. Carlton under Pagan did not improve much in the
2007 season, sitting at fourteenth on the ladder after Round 16, 2007 with four wins and twelve losses. Between Rounds 12 and 16, Carlton suffered five consecutive heavy defeats, the last of which was a 117-point defeat against the
Brisbane Lions at
the Gabba in Round 16, 2007. It proved to be the nail in the coffin for Pagan and his job, and Pagan was sacked as Carlton Football Club senior coach the following day on 23 July 2007. He was not bitter at the club's decision, and wanted to go on record that he would never have quit as the coach of the
Carlton Football Club. Pagan was replaced by assistant coach
Brett Ratten as caretaker senior coach for the remainder of the 2007 season, who was eventually appointed full-time senior coach of Carlton. Pagan had a year to go on his contract which was paid out in full by the club. In 2014, Pagan stated in the
Sydney Morning Herald newspaper that coaching Carlton was "a very difficult assignment", also taking into consideration the fact that the club had lost valuable draft picks in the wake of the salary cap breaches. In 2021, Pagan in a radio interview with
SEN described his tenure as senior coach of Carlton as a “snake pit” because of "Divisions and disunity" at the club that he experienced. In 2022, Pagan further elaborated by stating "When I was at Carlton I don't think I've ever seen a bigger mess. It was like going to work every day and a little bloke hiding behind the door with a sledgehammer and whacking you around the chin. They didn't have a great list, they didn't have any money, the place was in turmoil, there was factions and splits everywhere. It was a great club and it just disintegrated. It was the biggest regret without any doubt whatsoever". ==Post coaching-career==