The head of HM Revenue and Customs will step down in April amid criticism from MPs.
Homer joined HMRC in January 2012 and was awarded a damehood in the New Year's honours list.
But her tenure has been mired by criticism over her failure to answer calls from the public and her handling of the HSBC tax scandal.
Homer said she had decided to step down in April as it marks 10 years as a chief executive in the civil cervice and the start of the next spending review.
"HMRC has secured Ministerial support and funding for our ambitious transformation programme and it has the leadership team in place to deliver it," Homer said.
HMRC said that the process to appoint a new chief executive was underway.
Homer apologised in November after it was revealed that HMRC's giant call centre failed to answer a quarter of calls. The public accounts committee said that HMRC appeared "incapable of running a satisfactory service".
In February 2015, she was grilled by MPs over allegations that she failed to act on claims that HSBC avoided paying tax.
In a statement, Chancellor George Osborne said Homer had laid the foundations for HMRC to transform into world-leading digital service.
"She not only leaves behind a significantly more effective and efficient organisation, delivering more for less; she has also helped to transform HMRC into one of the most open, digitally-advanced revenue services in the world," Osborne said.
