Jane O'Hara will stand down from the role in December after three years overseeing the measurement of radio audiences.
O'Hara is leaving to spend time sailing in the Atlantic. Rajar has advertised for a replacement to be in place by the New Year.
Rajar, jointly owned by the BBC and the Commercial Radio Companies Association, has had a stormy few months in which it has endured a series of attacks from Kelvin MacKenzie, the chief executive of The Wireless Group.
MacKenzie wants Rajar to drop its diary-based system of audience research in favour of electronic measurement. Rajar will instead conduct further tests of new systems next summer.
O'Hara said that it was a good time to step down to allow her successor time to get to grips with the role before testing of electronic systems and the next review of the Rajar contract.
She said: "This has been a difficult decision. I thoroughly enjoy my role at Rajar. I wish I could do both, but I have decided to try my hand at ocean sailing."
MacKenzie said: "We didn't agree on anything - but personally, I liked her and I wish her all the best in the journey of a lifetime."
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