From August, Ms Homer will be director general of the Immigration & Nationality Directorate at the Home Office.
The directorate has responsibility for managed migration, border control, asylum, citizenship and nationality.
She will be charged with implementing the next stage of the government's comprehensive reform of the UK's immigration and asylum system.
Ms Homer's tenure in Birmingham has not been plain sailing. In April, a judge in the postal vote scandal found fault with aspects of the election in June 2004 in which she was returning officer, though he did not find she 'substantially' misconducted the election.
While she said Birmingham was 'a fantastic place', she added: 'I won't pretend it hasn't been a challenge.'
Her accomplishments include making the council's improvement more consistent across service areas and increasing customer focus.
But there is still 'loads' for her successor to do in Birmingham. 'This isn't a city where the job will ever be done,' she said. 'Achieving the improvements that we started in housing and social care is absolutely essential to everybody, but doing that without taking our eye off everything else at the same time.'
CV - Lin Homer
1982-1997 Worked at Hertfordshire CC in various posts ranging from a solicitor to deputy chief executive
1997 Became first woman chief executive at Suffolk CC
2002 Appointed chief executive of Birmingham City Council
2005 Becomes director general of the Immigration & Nationality Directorate at the Home Office