Thorne, who was recently nominated for three Bafta TV Awards, has also written the forthcoming play Harry Potter and the Cursed Child.
The writer said taking on the project was an "honour and privilege".
"The His Dark Materials trilogy are vast and glorious books full of beautiful characters," he added.
"I'm going to work as hard as I can to try and do justice to them."
The trilogy, partly set in a parallel universe, tells the story of a girl called Lyra who embarks on a quest to understand a mysterious phenomenon called Dust.
The books have been published in more than 40 languages and have sold almost 17.5 million copies worldwide.
The first novel, Northern Lights, was made into a 2007 feature film entitled The Golden Compass, starring Daniel Craig and Nicole Kidman.
Pullman said he was "delighted" to welcome Jack Thorne as writer.
"Jack is a writer of formidable energy and range, and I've greatly enjoyed talking to him and learning about his plans for bringing His Dark Materials to the screen," he added.
"I'm certain he'll do a superb job and I look forward to seeing the whole project develop as he shapes the story."
Thorne is establishing himself as one of Britain's most sought-after writers.  His credits include three of the This Is England series and the TV fantasy mini-series The Fades.
His plays include Mydidae, The Solid Life of Sugar Water and the stage adaptation of Let the Right One In.
He won best British newcomer at the London Film Festival for his first film The Scouting Book For Boys.
And last week Thorne's work was nominated for TV Baftas for best drama series -  for The Last Panthers  - best miniseries - for This is England '90 - and best single drama - for Don't Take My Baby.
His is currently working on a four-part miniseries for Channel 4 called National Treasure, starring Robbie Coltrane, Julie Walters and Andrea Riseborough.
The cast of His Dark Materials is yet to be revealed, but filming will take place in Wales.
Jack Thorne is to write the BBC TV adaptation of author Philip Pullman's epic trilogy of fantasy novels His Dark Materials.