Sir Jonathan Michael Thompson, KCB (born 29 December 1964) is a British civil servant who served as the Permanent Secretary of 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.

[4] Thompson was in local government as Finance Director for North Somerset Council.

[4] Thompson became Permanent Secretary of the MOD in 2012 succeeding Ursula Brennan who moved to the Ministry of Justice.

[7][8][9] Thompson was appointed a Knight Commander of the Order of the Bath (KCB) in the 2019 New Year Honours, "for public service.