Arnott's bread-and-butter "smart beta" or "fundamental indexation" strategy - systematically selecting, weighting, and rebalancing portfolio holdings on the basis of characteristics other than market capitalization - has been hugely successful.
Pimco, which had $1.59 trillion in assets under management on March 31, said it would not fill Maisonneuve's position.
In recent years, Pimco has tried to diversify its investor base to include those buying equity products and even tapped former Goldman Sachs banker Neel Kashkari, who ran the U.S. government's $700 billion Troubled Asset Relief Program, to direct an expansion into new markets, including stocks.
But the latest high-profile departure for Pimco, which has become synonymous with the U.S. debt markets, is yet another blow for the Newport Beach, California, firm.
"You don't think of Pimco when it comes to equity investing," said David Schawel, vice president and portfolio manager of Square 1 Financial. "They've been attempting this for years."
In September, Bill Gross, co-founder of Pacific Investment Management Co, left his post as chief investment officer and joined mutual fund management firm Janus Capital Group Inc , a move that followed record outflows from Pimco's flagship portfolio and his clash with other top executives.
Read MorePimco counters Bill Gross's 'short of a lifetime' call
His departure came just eight months after his top deputy, Mohamed El-Erian, stepped down.
"They remain primarily known as a bond shop, and assets in their bond funds have declined as investors were concerned with leadership changes ... and periods of underperformance," said Todd Rosenbluth, director of ETF & Mutual Fund Research at S&P Capital IQ.
Pimco's active and enhanced equities business has more than $50 billion in assets under management.
Maisonneuve will direct the transition, but "in light of these changes she has decided to leave the firm after a transition period," Hodge said.
Portfolio managers and analysts associated with the two Pimco equity strategies also will leave the firm.
Pimco brought in Maisonneuve in January 2014 as one of six deputy chief investment officers.