Owen said it was a “difficult” decision to leave, but added she has been offered a “one-off opportunity to try a different career in the private sector".
She joined HMRC to lead personal tax in 2012, before taking charge of customer services last year.
An interim will be appointed soon and the Revenue will advertise for the job “very shortly”, according to an internal staff announcement.
Before joining HMRC, Owen was work services director and deputy chief operating officer at the Department for Work and Pensions. She was previously COO in Jobcentre Plus and had two spells in the private sector on secondment.
“I have loved my time in HMRC and I leave feeling immensely proud of what we have achieved. The last five years have seen some significant changes in the service we provide to our customers, the way we think about our customers as well as how we do business and how we work together,” said Owen.
The Revenue has struggled significantly in recent years with its customer service performance as its budgets have been cut steadily since 2010.
In December last year a report form the Public Accounts Committee warned HMRC that its planned staff cuts could lead to a “disastrous” further decline in service standards. It was argued that HMRC did not have a credible plan to make savings without damaging customer service. While the number of complaints received were reaching the highest level since the 2008 financial crisis.
Jon Thompson, HMRC chief executive, said that Owen will be “hard to replace.”