Fly half Farrell led his country to third place at the recent Rugby World Cup in France but was the subject of boos from his own fans on several occasions having missed the first two games due to suspension.
He finished as the leading point-scorer at the tournament with 75, and put on a masterful display in their 16-15 loss to eventual champions South Africa in the semi-finals that almost got his side over the line.
"Everyone at England Rugby is fully behind Owen’s decision," England coach Steve Borthwick said.
"Since making his debut, he has been an integral part of the England set-up for over a decade and the demands on elite athletes are extremely challenging.
"He is an exemplary player, captain and leader and always gives his all for his country.
"It is with typical courage that Owen has made this decision to open up in this manner. Together with all of us at England Rugby, I will do everything I can to ensure that he has the support he requires going forward."
Saracens confirmed that Farrell will continue to play for them.
"As always, Owen will have the full support of everyone at the club," they said in a statement.
Farrell was suspended and criticised on social media ahead of the World Cup following a red card for a dangerous tackle in a warm-up fixture against Wales, which led to him missing England's first two games against Argentina and Japan.
The card was first rescinded by an independent disciplinary committee before an appeal from World Rugby against the decision resulted in a four-game ban.
Father Andy described the social media vilification of his son as "disgusting" and a "circus".
Owen Farrell has played 112 tests for England and six for the British & Irish Lions since making his international debut in 2012.
He is third on England's all-time list behind Ben Youngs (127) and Jason Leonard (114). He is England's leading points-scorer in tests with 1,237.
