Athow will succeed the outgoing Ruth Stanier in the role as she undertakes a 12-month career break.
Effective from the beginning of October, Athow joins HMRC from his current position as deputy national statistician and director general for economic statistics at the ONS.
He said: “I am excited to be joining HMRC and customer strategy and tax design at this important time.
“It is a department that has done so much to support the country during the pandemic and will be hugely important as the economy recovers in providing the taxation to fund our public services and supporting businesses and people across the UK.”
Jim Harra, chief executive and first permanent secretary at HMRC, added: “I’m pleased that Jonathan Athow will be stepping into this critical leadership role working to build a trusted, modern tax administration system – one that brings in revenue for public services, makes it easy to get it right, is valued and trusted.”