The move marks a return to Emap for Thompson, formerly promotions operations manager across all Emap's radio stations. She left the company three years ago to help launch Bath FM, where she was also managing director.
She replaces Roz Whitney, who left Emap to spend time with her family.
Thompson's career in radio began in 1986 when she joined LBC as a secretary. After six months, she moved to publicity and promotions executive and, in 1989, she joined Fox FM as promotions manager.
In 1995, she became head of promotions and sponsorship at LNR and moved to Talk Radio three years later. From there, she joined Emap.
Michelle Surrell, managing director of Emap Performance North, said: "I am delighted to be welcoming Alexis back to Emap. She has taken Bath FM from its launch three years ago to market leader and I am sure she will be a fantastic person to lead the great team in Leeds."
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