Brown is likely to return after a hamstring injury while Thomson is available after missing the Tennent's Scottish Cup draw at Aberdeen through suspension.
The return of the pair would be a huge boost to a Hibs side reeling from news of the Achilles injury to striker Chris Killen that has ruled the New Zealander out for the rest of the season.
Fowler, whose side will move level on points with Hibs if they win the encounter, said: "Hibs are going well even though Chris Killen will be a big loss to them after his injury.
"Scott Brown and Kevin Thomson will be back for them so it will be tough.
"Those two are as good as you'll come up against in the SPL, especially Thomson.
"He builds everything for them while Brown is more dynamic and likes to get forward. I'll probably need to match Scott's runs from midfield."
Fowler has excelled in the midfield anchorman role since being converted from a right-back by Killie boss Jim Jefferies.
His form earned him praise from former Scotland boss and new Rangers chief Walter Smith while press reports claimed Celtic were interested in a move for the 26-year-old.
But Fowler laughed off the Parkhead rumours and is more concerned with turning around Killie's mid-season slump.
He said: "I've done okay this season but it doesn't matter how well I've been playing - we're without a win in five games and out of the Scottish Cup.
"I heard the Celtic story and it was totally out of the blue. I just had a laugh about it.
"I haven't heard anything and I've laughed it off. The boys have made a joke about it.
"I'm treating it as pure speculation. It's nice if people are taking notice but I don't know if they are.
"As long as I'm playing and the gaffer is happy, I'm happy.
"I feel I could play at that level but we'll see what happens. I'm just happy where I am because I'm still learning."