Al-Khelaifi said on Thursday that the ECA would welcome Juventus back after the club signalled they will pull out of the European Super League project.
The ECA represents more than 440 clubs across the continent, although it is dominated by the big teams, including nine of the 12 initially involved in the planned breakaway Super League.
Juventus, however, said they were not looking to rejoin.
"Juventus FC is not assessing the possibility to rejoin ECA at the moment," the club's press office told Reuters in an email.
"If they stop what they are trying to fight for, which I think is a stupid project, they are always most welcome," Al-Khelaifi told reporters after an ECA board meeting in Copenhagen.
"I spoke to the owner and, you know, he called me and I think they want to be back. They are definitely most welcome," Al-Khelaifi said.
Al-Khelaifi, who is also president of French champions Paris Saint Germain, took over as ECA chairman when former Juventus chairman Andrea Agnelli, who had supported the idea of a European Super League, stepped down in 2021.
Agnelli and the Juve board resigned in November last year.