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Wilkinson, who has led an ambitious transformation programme at the Home Office since February 2015, will take up her new role at NHS Digital in June.
At NHS Digital she will be at the helm of delivering a paperless NHS by 2020, which includes a large portfolio of programmes at national and local level focused on making effective use of information, technology and data.
NHS Digital chair Noel Gordon said in a statement that he was "delighted" to have Wilkinson on board.
"Sarah brings vast experience of implementing complex technology projects, alongside a deep insight into bringing about positive change to a broad range of communities through digital delivery," he said.
"She is joining a talented, ambitious and committed team and I look forward to seeing NHS Digital continue to work with the health and care sector to deliver technology and digital services of maximum value to patients and the public.
In an email, seen by Computer Weekly, Wilkinson told the Home Office digital, data and technology (DDaT) team that although she was sad to leave the department, the role as CEO of NHS Digital was “too attractive an opportunity to turn down”.
Wilkinson has been driving change at the Home Office since she took on the role, and last year led the department – which is responsible for a range of digital and technology projects, including the e-Borders successor programme and the IT of several arm’s length bodies – through a merger of its digital (HOD) and technology (HOT) units.
The new team combines 250 staff from the HOD unit, with about 1,000 employees and contractors in HOT, and has allowed the Home Office to streamline work and utilise skills across both organisations.
In an interview with Computer Weekly in February, Wilkinson said there was still a lot of work to be done, but the department had come a long way in the past few years.
NHS Digital chief operating officer Rob Shaw has been functioning as interim CEO since Williams' departure.