Thompson will make the move from HMRC, where he has been chief executive and first permanent secretary since April 2016.
He said: “It’s been a tremendous privilege to lead HMRC for more than three years, so to leave now has not been an easy decision for me to make.
“However, to have the opportunity to lead Financial Reporting Council, as it turns into the Audit, Governance and Reporting Authority, and promote public trust in doing business in the UK, at a point when we’re about to forge new alliances across the world, is too exciting to turn down.”
The decision to reform the FRC, which regulates auditors, accountants and actuaries, was taken following the Kingman Review and gave the AGRA new powers to conduct “more comprehensive, visible reviews for greater transparency”.
During his time at the HMRC, Thompson presided over record increases in collection of tax revenues, introducing the Making Tax Digital scheme and opening HMRC’s first regional centre, the government said.
CIPFA chief executive Rob Whiteman congratulated Thompson via Twitter and noted that CIPFA alumni were “flourishing” with the recent appointment of Gareth Davies as auditor general as well as earlier appointments of Mike Driver to the government finance function and Elizabeth Honer to the Government Internal Audit Agency.
Thompson revealed to an Institute for Government event last year that he had received death threats after suggesting that a potential post-Brexit customs arrangement could cost the UK £20bn.
He also received a knighthood in this year’s New Year Honours.
Mark Sedwill, cabinet secretary and head of the civil service, said: “I am grateful for the enormous contribution Sir Jonathan has made during his time at HMRC.
“During his tenure, we’ve seen year-on-year increases in the revenue collected, which critically goes into funding our public services.”
