The Argentine returned to training on Tuesday after suffering a thigh injury in Saturday’s 2-2 draw with Valencia.
“It is true that sometimes we have had doubts with players and we have waited until the last moment,” said manager Ernesto Valverde.
“It’s the same with Messi.”
Wednesday’s tie at the Nou Camp will be the first of three El Clasico’s in 25 days, with the second leg on Wednesday, 27 February and a La Liga encounter on Saturday, 2 March.
Forward Ousmane Dembele is also unlikely to be fit for the first leg at the Nou Camp, as he is still recovering from a hamstring injury.
Real Madrid have everyone available apart from defender Jesus Vallejo, who is out with a muscular issue.