The 22-year-old is receiving treatment for severe bruising to his leg and knee suffered in the draw with Birmingham on Saturday and did not train on Tuesday.
Barca playmaker Andres Iniesta has been ruled out with a hamstring injury.
The 25-year-old came off at half-time in the Spanish side's 1-0 league win over Real Mallorca on Saturday.
Fabregas, who was with Barcelona in his early teens, has told Arsenal boss Arsene Wenger he is desperate to play in the match.
"The medical staff tell me there is still a chance he will be available but that will decided in the warm-up, which tells you how late we will leave it," said Wenger.
"I would say 60 per cent against, 40 per cent for him playing."
The Spanish midfielder required lengthy treatment following a challenge by Craig Gardner at St Andrew's but carried on to complete the match, as a late Kevin Phillips equaliser dented Arsenal's title hopes.
Wenger must now rally his side for the match against Barcelona, who won an unprecedented treble of Spanish league, cup and Champions League last season.
"Will it be hard to lift the players up for Barcelona? Yes, it is always hard to pick the players up when you get caught like that at the end of a game," stated Wenger.
"We are on a run that is very difficult and where we have no room for error at all so the result at Birmingham was a big disappointment.
"It felt like a defeat but the game against Barcelona is in a different competition and we have a few days to recover and prepare."
Barcelona have their own injury problems after it was revealed Spain international Iniesta will be sidelined for about 10 days.
He faces a race to be fit for the home leg against Arsenal on 6 April and the clash with Real Madrid in two weeks.
Iniesta was one of the stars of last season's Champions League, scoring a stoppage-time winner in the semi-final at Stamford Bridge and producing a performance against Manchester United in the final that prompted Wayne Rooney to describe him as the best player in the world.
The meeting of Arsenal and Barcelona is a repeat of the 2006 final - which Barca won 2-1 - and has several other sub-plots.
Fabregas is desperate to face the club where he was nurtured before leaving to join Arsenal at 16, while Barcelona striker Thierry Henry will be up against the team for which he scored 226 goals.
"I'm very emotional but also staying calm," revealed Henry. "It will be a strange game for me.
"Before the draw I said that I did not want to face Arsenal. That was my wish but now that's the game we've got and we'll have to give everything.
"It's very special. To return home is strange and even more so in the quarter-finals of the Champions League."
Should he be passed fit, Fabregas will take on his boyhood club, where he played in the same youth team as Barca duo Lionel Messi and Gerard Pique.
"I know they will be two exciting games," he said.
"We will, of course, give everything and you know if you want to win the competition you have to be ready to play anyone."
Source: BBC
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