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Thompson was made a Knight Commander of the Order of the Bath (KCB) in the 2019 New Year Honours list.

In 2015 Thompson was paid a salary of between £165,000 and £169,999 by the MOD, making him one of the 328 most highly paid people in the British public sector at that time.

Sir Jonathan Michael "Jon" Thompson, KCB is a British civil servant who served as the Permanent Secretary at the Ministry of Defence (MOD) from September 2012 until April 2016, when he succeeded Dame Lin Homer as Permanent Secretary and Chief Executive of HM Revenue and Customs. He became Chief Executive of the Financial Reporting Council after leaving HMRC in Autumn 2019.

Thompson joined the Civil Service in 2004, as OFSTED’s first finance director. He moved to Department for Education and Skills as their Director-General for Corporate Services in 2006, leaving the then Department for Children, Schools and Families to join the Ministry of Defence (MOD) as Director General of Finance in 2009. Thompson became Permanent Secretary of the MOD in 2012 succeeding Ursula Brennan who moved to the Ministry of Justice. He then became Chief Executive and First Permanent Secretary of HM Revenue and Customs. Thompson is currently the Chief Executive of the Financial Reporting Council.

Thompson was born in Norwich, and educated at Earlham High School, Norwich City College and Anglia Polytechnic, which later became Anglia Ruskin University. He became CIPFA qualified in 1989.

Thompson married his wife Dawn in 1987 and has three sons and one grandson. He is a supporter of Norwich City Football Club, and lives in Cambridgeshire.