The all-rounder will leave the UK later this week and travel to New Zealand to be with his parents.
He will miss the second test match against Pakistan, starting on Thursday and the third, which starts on August 21.
Both are played at the Ageas Bowl in Southampton.
The England and Wales Cricket Council said in a statement: “The versatile England Ben Stokes will miss the rest of the #raisethebat test series against Pakistan for family reasons.
“Stokes will be leaving the UK later this week and heading to New Zealand. He will miss England’s two tryouts against Pakistan at the Ageas Bowl starting Thursday 13 August and Friday 21 August.
“The England and Wales Cricket Board, along with the Stokes family, are asking that all media respect the privacy of the family at this time. ”
England lead the three-game series 1-0 after a memorable three-wicket victory at Emirates Old Trafford on Saturday.
England vice-captain Stokes has already had a huge impact on the summer so far, leading the team against the West Indies in Southampton and then helping to set up the 2-1 Series victory in averaging 90 with the bat and claiming nine wickets with the Ball.
But after Saturday’s victory in a game where he took two wickets after ignoring a thigh injury, Stokes told his teammates he would now leave the biosecurity bubble and fly to Christchurch to join his family .
The 29-year-old father, Ged, suffered serious illness after arriving in South Africa ahead of the 3-1 win of the winter series before returning to New Zealand to continue his recovery.
Stokes was not the only England player with no-play issues in mind.
Jos Buttler, whose 75 on the final day was a big part of England’s unlikely victory, played despite his father being rushed to hospital the night before.
Last summer, Stokes contested the decisive heats as England beat New Zealand in the Cricket World Cup final and beat a hundred wins to secure a victory for the Ashes.
In 2018 he was acquitted of the brawl after a scuffle outside a Bristol nightclub the year before.
England’s test series against Pakistan is live on Sky Sports.