The 2002 – 2003 campaign proved to be a decent one for the Pilgrims as they were in emphatic form in the second division, narrowly missing out on a birth in the play offs as they finished the campaign off in a very impressive eighth position. The following year saw Plymouth Argyle being crowned second division champions as they enjoyed triumph in winning the division. They gained ninety points by the end of the campaign and were in the second tier of English football for the first time in 12 years.
Their first season in the new division saw the club finish off in 17th position in the new Coca Coal Championship. They crashed out of the League cup in the first round as they suffered defeat against Yeovil Town in the competition.
The 2005 – 2006 season saw the Pilgrims start off the season in great form and they finished it off in a very decent 14th position finish. They crashed out of the FA cup in the third round as they suffered defeat against Wolves and they were eliminated out of the league cup in the second round as they crashed out after suffering defeat against league two side, Barnet FC.