The change at the top will come as Bill Thompson retires as head of the number-one global bond manager later this year.
Mr El-Erian, 50, is currently the firm's co-chief investment officer, along with managing director Bill Gross.
He is anticipated to keep hold of this position, in addition to taking on Pimco's chief executive duties.
Prior to re-joining the bond manager in January, Mr El-Erian ran Harvard University's $35 billion endowment fund.
Based in Newport Beach, California, the firm currently retains 1,000 employees - and $840 billion of assets - around the world.
Writing in his latest book, Mr El-Erian expressed the belief that the world's economy is re-aligning, with wealth shifting from the US to emerging markets in India and China, Bloomberg reports.
"For those seeking to understand global economic and financial developments, it will no longer be sufficient to get the United States, Europe and Japan right," he commented.