The 28-year-old enjoyed an impressive season at Camp Nou, scoring 14 goals and providing 14 assists in 49 appearances across all competitions.
Rashford also helped Barcelona win the LaLiga title during his campaign in Spain.
However, the Catalan giants opted against signing him permanently, instead investing in England international Anthony Gordon from Newcastle United.
The England international is now set to return to Manchester United, with Flick acknowledging his departure will be felt by Barcelona ahead of the new season.
"What I can say about Marcus is I appreciated working with him.” Flick told the media after Barcelona’s match against Birmingham City.
"Sometimes it’s not always you don’t know what happens with players who are on loan.
"Our situation also is not easy, but I appreciate him a lot working with him; he’s a fantastic player, a fantastic person.
"I think also the team miss him; I will miss him, but that’s life."