The Brazilian missed Monday's Barclays Premier League defeat by Chelsea with a muscle strain and is expected to be sidelined for at least another fortnight.
City host Barca in the first leg of their last-16 tie at the Etihad Stadium on February 18.
Manager Manuel Pellegrini said: "Fernandinho is working with the physiotherapist, maybe he will be at least 15 days more.
"It is difficult (for Barcelona). We will see in the next week but it is difficult."
Fernandinho, who was sorely missed in the 1-0 loss to the Londoners, joins two other key players in Sergio Aguero and Samir Nasri on the sidelines.
Aguero, top scorer with 26 goals this season, is expected to be out until the end of the month with a hamstring problem.
Pellegrini said: "The same thing. He is working with the physiotherapist.
"He has started running but he will not be available for Barcelona."
Nasri was ruled out for six to eight weeks after suffering knee ligament damage in the victory at Newcastle on January 12.
"Samir is working well, I think that next week, maybe in the middle of the week he will be working as normal with the squad," said Pellegrini.
Nasri, 26, who was signed from Arsenal for £24million in 2011, comes to the end of his contract at the end of next season.
Asked if discussions over a new deal were to begin, Pellegrini said: "Not in this moment, it is not our first concern.
"I think Samir is a very good player, that he is having a very good season with us. We will see what happens in the future."