The 73-year-old veteran performer will take over from Tobias Menzies, who portrayed the Duke of Edinburgh in series three and will reprise the role for the upcoming fourth series.
Matt Smith was the original actor playing Philip in the first two series, appearing alongside Claire Foy as Queen Elizabeth II.
Imelda Staunton will play the Queen in the final pair of series, taking over from Olivia Colman, who won a Golden Globe for her performance.
Lesley Manville has also been confirmed for series five and six as Princess Margaret.
Pryce has had a varied career on both stage and screen, winning two Tony Awards and securing his first Oscar nomination this year for playing Pope Francis in The Two Popes.
On the small screen, he is best known for playing religious leader The High Sparrow in Game of Thrones.
Read more: Trailer for The Two Popes
In a statement shared on Twitter, Pryce said he is “delighted” to be collaborating with Netflix again.
More news from the palace: Jonathan Pryce will play Prince Philip in the final two seasons of The Crown (S5 and 6)! pic.twitter.com/Wy3ctihtA5— Netflix UK & Ireland (@NetflixUK) August 13, 2020
He added: “The positive experience I had making The Two Popes has given me the confidence to tackle the daunting prospect of portraying Prince Philip.”
The Crown is set to return later this year for its fourth series, having completed the lion’s share of its filming before coronavirus caused TV and film productions to shut down all over the world.
Cast members were able to help complete the series from quarantine, sending extra voice work through to the production team via their smartphones.
While series four of The Crown will not be affected by the coronavirus, the fifth series has been delayed and will not air until 2022.
Deadline reported that this delay had always been planned and was not a result of the pandemic.
Read more: The Crown and Chernobyl lead BAFTA noms
The fourth series of The Crown will be set during the 1980s, with Gillian Anderson portraying divisive prime minister Margaret Thatcher.
The final two series are set to feature events extending into the early part of the 21st century, likely including the death of Princess Margaret and the Queen’s Golden Jubilee in 2002.