Roger Wright, who has a distinguished background in the classical music world, will succeed Nicholas Kenyon, who was appointed controller of BBC Proms and Millennium Programmes in July.
Mr Wright's main rival for the post, Roger Lewis, president of Decca Records, was yesterday confirmed as the new head of Classic FM, which recently recorded its highest listener figures.
There had been widespread speculation that Mr Lewis was in line for the Radio 3 job. But the corporation opted for the more traditional Mr Wright, 42, who has been head of BBC Classical Music since that post was created in March 1997.
"I am delighted to have been given the exciting and daunting challenge of running Radio 3," Mr Wright said yesterday. "I look forward to developing the quality work of my distinguished predecessors."
A spokeswoman for the station said: "It's very good news ... He will maintain the cultural high ground."
Will Wyatt, director of BBC Broadcast, said of Mr Wright: "The network is in good and sensitive hands."Reuse content