Mr Anderson previously was the AFA's chief operating officer from 2011 to 2015 before a stint as Netwealth's general manager for governance and advice, according to a statement.
He replaces Samantha Clarke, who resigned last month to pursue her RegTech business, and will start in the role on 19 June, the statement said.
Mr Anderson will be leading a team that includes Linda Vogel, who was recently appointed general counsel.
AFA chief executive Philip Kewin said, "Phil has a tried and proven track record in the field of policy and professionalism and a passion for advice that we believe will assist the AFA and its members take advice in Australia to the next level.
"The AFA wants to ensure the advice profession moves forward, with decisive and progressive action around policy, professionalism, advocacy and influence at all levels to ensure this journey continues to lay a strong foundation in meeting consumer expectations."
Mr Anderson commented on his return that the AFA is a place where he can "make a real difference in the process of making financial advice a recognised profession".
"This is a challenging and exciting time for the profession as we progress with the implementation of the professional standards legislation," he said.
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