Recent reports claimed that Riise, 32, was set to leave Craven Cottage after reacting angrily to being omitted from the first-team in recent weeks.
The former Liverpool man, who started 35 league games last season, has not featured for Fulham since the 1-1 draw with Southampton on Boxing Day and was an unused substitute in subsequent fixtures against Swansea City, Wigan and Blackpool.
However, Jol insists his relationship with the full-back is good and says he should fight for his place at the club.
He said: "My relationship was fantastic and is probably still OK. It's the same all the time in England. I never had a bust-up, I had a conversation.
"There's no problem, I just wanted to change things. He wants to fight for his place like any player."