Mavor, who has been chief executive of the NTS since 2009, will join English Heritage in May, when the existing organisation will be split into a charity of the same name that will manage the national heritage collection of more than 400 historic sites, and Historic England, the arm of the organisation responsible for planning and heritage protection that will remain within government.
Before joining the NTS, Mavor was chief executive of the youth volunteering programme Project Scotland.
Simon Thurley, who has been chief executive of English Heritage in its current form for the past 13 years, will step down when the organisation separates to take up a senior research fellowship at the Institute of Historical Research.
Sir Tim Laurence, chair of the English Heritage charity, said Mavor would bring a wealth of experience from within and outside the heritage sector.
"This is an exciting moment in the history of the organisation as we become a charity," he said. "Years of planning and success have brought us to this point. Bringing history to life for millions of people each year and caring for such important historic sites is a huge privilege. Kate is exactly the right person to lead the new charity at this important time."
Mavor said: "It is a privilege to lead English Heritage on the first stage of its new journey as a charity. English Heritage looks after sites where significant moments in history happened. Individually and collectively, these precious places tell a remarkable story. I look forward to building on the great successes of my predecessors."
A spokesman for English Heritage was unable to confirm how much Mavor would be paid.
English Heritage will receive an £80m government grant to make improvements to the national heritage collection – which includes Stonehenge, Kenilworth Castle in Warwickshire and parts of Hadrian’s Wall – with the aim of the charity being self-sufficient by 2023.