The Rugby Park outfit are in 11th place in the Clydesdale Bank Premier League after a poor season marred by injuries and loss of form.
Killie manager Jim Jefferies has vowed to strengthen his squad over the summer with new signings and Fowler believes the Ayrshire outfit will not endure another poor season.
Fowler said: "Hopefully we'll regroup over the summer.
"The majority of this squad has got us into the top six in the past two seasons and hopefully we'll come back raring to go next year.
"We've had a disappointing season but before that we were flying high with two fifth place finishes.
"Hopefully if we replace the players that have left then we can push on again.
"It looks like we'll finish 11th this season unless we win our last two games and St Mirren don't win any.
"It's been a disappointing season as we've been really inconsistent.
"We're already looking to next season and hopefully the manager can bring in one or two players and freshen things up."
Fowler admits he has never experienced a campaign where the club have been hit so hard by injuries.
He said: "In previous seasons our team has picked itself but this year there's been a lot of changes through injuries.
"That can happen and it seems to be our turn but hopefully it'll be someone else next season.
"This is the worst I've known as the whole squad has been affected and everyone's been injured at some point."