The Croatia international has enjoyed a remarkable season with the Europa League champions, having scored 13 goals and picked up 12 assists in the league and in Europe.
His excellent performances have seen him linked to several elite clubs throughout the season and reports have emerged that Barcelona are close to agreeing a deal with Sevilla to see the 26-year-old join the Catalan giants this summer.
And Emery has admitted that his side are likely to lose the midfielder, but insisted they have to be prepared for his departure.
"The best thing from a sporting sense is that Rakitic stay with us, but I understand that for various reasons Rakitic will go," he told Canal+ Liga.
"And we have to be prepared for it. If he finally leaves, we have to work hard to get another Rakitic."