Pereira, who was formerly Slavisa Jokanovic's assistant manager at Craven Cottage, returned to the club in January and helped Scott Parker's side return to the Premier League.
“Fulham is a club I will always hold a lot of affection for, the staff and supporters have been truly wonderful and I have made many friends for life," said Pereira.
“I would like to thank Mr Khan and Tony Khan for the incredible support they have given to me. The most important thing to me is to be leaving the Club at a time when its objective of being promoted to the Premier League was achieved.
“I will be keeping a keen interest in Fulham and I will be cheering for the team this season. I wish the Club every success and hopefully our paths will cross again in the future.”
— Fulham Football Club (@FulhamFC)September 24, 2020
Meanwhile, Fulham are close to completing the signing for former Barcelona defender Marlon Santos from Sassuolo. Having conceded seven goals in their opening two Premier League games, Parker is keen to add numbers at the heart of defence.