The secretary general of the federal AMA, Francis Sullivan, will take up the Catholic Church post after five years with the medical lobby group.
The announcement from the AMA did not specify Mr Sullivan's new role, but the Australian Catholic Bishops Conference and Catholic Religious Australia announced last month they would establish a 10-member council of lay people and members of the clergy and the church was due to announce the head of that council on Wednesday.
AMA president Steve Hambleton described his departing colleague as a "highly respected advocate".
"It is with much regret that the AMA is losing such a strong and well-connected colleague, but he is taking on a role for which he is uniquely equipped and very passionate about," Dr Hambleton said in a statement on Wednesday.
"Francis has been a diligent and hardworking leader and manager for the AMA. "He has not only been a trusted CEO and adviser to the AMA leadership, he has been a friend and confidant."
Before joining the AMA, Mr Sullivan spent 14 years as the chief executive officer of Catholic Health Australia.