Gavin Calver will take up the post as Director of Mission/England at the EA in June next year.
Speaking about the move he said: "After six years as national director, and 13 years at YFC, I feel the time is right for me to move on from this role.
"I feel God has called me to serve the local Church by helping to mobilise mission across England.
"I am passionate about seeing the local Church fulfil its calling to take the gospel of Jesus - in both words and deeds - into every community in the land."
Gavin Calver's main responsibilities will include developing ways for EA member organisations to work together.
Steve Clifford, general director of the Evangelical Alliance, said: "We are delighted that Gavin will be joining our leadership team.
"His passion for serving God through the Church coupled with his vision for evangelism will be such an asset to our movement.
"His appointment will open up a new chapter in our journey as we seek to support churches as they reach out to their communities."
The post being taken up became vacant after Dr Krish Kandiah left to become president of the London School of Theology.
Youth for Christ is now searching for a new National Director and is encouraging applications.
Meanwhile, the Evangelical Alliance the first ever black female director in its 168-year history.
Chine Mbubaegbu, former head of media and communications, has been appointed as a director of communications for the Alliance.
Speaking about the appointment she said: "I have been privileged to work for this amazing organisation for the past four years and am looking forward to bringing a different perspective to the leadership team.
Listen to Gavin Calver speaking about his move with Premier's Marcus Jones.