Dr Irene Bishop, headteacher of St Saviour's and St Olave's School, is to retire at Easter 2013.
Dr Bishop, headteacher of the girls' secondary school at Bricklayers Arms for more than a decade, received the CBE in the Queen's birthday honours list this year.
"I have enjoyed every moment of my headship; working with such a committed and hardworking team of teachers and support staff has been a blessing," said Dr Bishop in a message published in the Southwark Cathedral newsletter this week.
"I have been a practising Christian since childhood but working in a church school was new to me. The Christian ethos, central to everything we do, is extremely powerful.
"My faith has been nurtured and has grown since starting here. St Saviour's has been central to my life for a very long time. I will always hold it close to my heart."