Stokes, who plays for England across all three formats as well as in the Indian Premier League, has opted to “prioritise his mental wellbeing” and to rest his left index finger which has been an issue in recent times.
The England and Wales Cricket Board (ECB) statement said: “The ECB fully supports Ben’s decision, and we will continue to help him during this period away from the game.”
The announcement comes ahead of England’s Test series against India starting next week.
The two nations are due to play five Tests across August and September, starting at Nottingham’s Trent Bridge on August 4.
England managing director of cricket Ashley Giles said: “Our primary focus has always been and will continue to be the mental health and welfare of all of our people.
“The demands on our athletes to prepare and play elite sport are relentless in a typical environment, but the ongoing pandemic has acutely compounded this.
“Spending significant amounts of time away from family, with minimal freedoms, is extremely challenging.
“The cumulative effect of operating almost continuously in these environments over the last 16 months has had a major impact on everyone’s wellbeing.”
Stokes has also endured personal challenges, with his father Ged passing away from brain cancer in December.
The all-rounder had taken leave from the national team last year to travel to New Zealand to be with his father.