According to Josephus, in A.D. 62 James was charged with breaking the Law. He was tried by the Sanhedrin and stoned to death. After Festus died, Albinus was appointed procurator. Ananus was High Priest at the time, and he arrested James after Festus’ death but before Abinus arrived in Caesarea. As a result, Agrippa deposed Ananus after only three months as High Priest. (Antiq. 20.197-203).
The story of James’ martyrdom appears in Heggesippus, although with considerable expansions. Because of his great reputation as a righteous man, James is given an opportunity to address the crowds at Passover in order to address the problem of Jesus as messiah. James is lead to the top of the temple stairs and proceeds to preach the gospel and convince many. The Sadducees and Pharisees realize their mistake, and shove him down the stairs, although he is not killed. People in the crowd therefore take a fuller’s brush and beat him to death.
A final version of the story appears in the Pseudo-Clementine literature. There James is assaulted by an enemy and thrown down the stairs. The enemy, as it turns out, is Paul. In this literature Paul is an enemy of real Christianity, as represented by James. He is in fact often described in terms of Simon Magus.
Out of this data it is certain that James died in 62 at the hands of the Sanhedrin. What is remarkable is that he was accused of being in breach of the Law. While it is clear from the New Testament and James that he was clearly in favor of the Law, it is possible that his belief in Jesus as the Messiah and his occasional contact with Hellenistic Jews (like Paul) was interpreted as radical, given the volatile context of the mid-60’s, leading up to the Jewish War.