During his elite career from 1989 to 1999 he represented Start and Strømsgodset, being best known for saving the latter club from relegation the last minutes of the 1996 Eliteserien.
In that tournament, Dagbladet praised Isaksen as man of the match against guest competitor England U15.
In the latter tournament, Norway qualified for the 1989 FIFA World Youth Championship, where Isaksen again participated.
[9] Isaksen broke his leg in 1991 and did not return until the fall of 1992, missing the 1991 Norwegian Football Cup final.
[12] As Strømsgodset finished second in the 1995 1. divisjon, Group 2, the team reached a promotion playoff against Sogndal.
[15][16] Isaksen was known for a fierce and temperamental playing style, which led him to be a powerful duel player, but also pick up a lot of yellow cards.
[19] In 1998, Isaksen was reported by Lyn for verbal abuse towards their player Hassan El Fakiri at the La Manga friendly tournament.
Two minutes into stoppage time, Isaksen sent the ball past Frode Olsen to increase the lead to 6–2.
[29] Ahead of the 1997 season, Isaksen had concrete offers from Strømsgodset, Start, Hødd and Aalesund, should he choose to move to Sunnmøre where his wife was from.
Though Start was now relegated, Isaksen would play an important role in their attempt at re-promotion, and would also be close to family in Kristiansand.
Isaksen also tried to activate a clause in one of his former contracts, which stated that he was personally entitled to 15% of the transfer fee received by Strømsgodset.
After the 1998 season, Isaksen was not willing to accept a pay cut, and Start wanted to terminate his contract.
An attempt to find another club in Norway or England, aided by the Norwegian Players' Association, was fruitless.
[34][35][36] Despite an offer from Aalesunds FK,[37] Isaksen remained in Start, ultimately accepting the purported pay cut.
He first joined the seventh-tier club FK Grim together with another former Start player Tore Løvland to play football as a hobby.
Here, he worked as a sales director in a power company and coached the youth team of his son.