Lee, who is leaving the Small Charities Coalition at the end of the year and relocating to West Yorkshire with her family, will take up her new post on 7 January. She takes over from Frank Plumbridge, who died earlier this year.
The charity, which supports families with learning disabilities in Leeds, celebrates its 60th anniversary in 2013.
Martin Staniforth, Leeds Mencap’s chair of trustees, welcomed Lee’s appointment. "Her skills and experience will ensure that we continue to develop and improve the vital services we provide in the city," he said.
It was announced earlier this month that Alex Swallow, the founder of Young Charity Trustees, will be the next chief executive of the Small Charities Coalition.