In a recent interview with the Irish Examiner, Isaac Hempstead-Wright confirmed his return as Bran Stark for the sixth season of Game of Thrones. Isaac said:
I can’t say a lot but I am back this season, and it’s going to get particularly interesting with Bran. He has some interesting visions.
Now this should come as no surprise, since we already had Dan and David's plan for Bran laid out before the start of the fifth season. When Benioff talked to Entertainment Weekly, he explained Bran's absence from the fifth season by saying:
Like, it would be far less interesting, after The Empire Strikes Back to have an hour-long movie in between Empire and Return of the Jedi where Luke is training. It’s so much cooler to cut from end of Empire to begging of Return, where he’s become the Jedi.