Dr Krish Kandiah is taking up a job at the London School of Theology.
He first joined the EA in 2007 and had been Executive Director for Churches in Mission and England.
He takes up the role of president at the London School of Theology in October.
He said: "I count it an incredible privilege to join the team at LST, a college which has helped shape so much of the evangelical landscape in the UK and beyond.
"I am looking forward to helping Christians develop a richer and deeper understanding of our faith so we are better able to share it with bold humility.
"I have loved being on the leadership team at the Evangelical Alliance over the past few years and have been privileged to play a part in serving the Church across the UK.
Steve Clifford, general director of the Evangelical Alliance, said: "We are delighted for Krish and excited for him as he takes up this fantastic position at one of our member organisations.
"Strong links already exist between LST and the Alliance, with myself and my two predecessors Joel Edwards and Clive Calver having been trained there.
"This is not goodbye. In fact, we look forward to forging even closer relationships in the coming years."
Hear Krish compare his appointment to Liverpool Football Club signing Mario Balotelli: