Gross, 70, will manage the recently launched Janus Global Unconstrained Bond Fund and will join the Janus team focused on global asset allocation. Gross will begin managing the fund and related strategies effective Oct. 6, 2014, the company said.
"Bill Gross has an exemplary track record with decades of success and he will offer an exceptional approach to navigating today's increasingly risky markets with a focus on macro, unconstrained strategies. His involvement provides Janus a unique opportunity to offer strategies and products that are highly complementary to those already managed by our credit-based fixed income team," Richard Weil, CEO of Janus Capital, said in a statement.
A spokesman at Allianz, Pimco's parent company, said it would not be commenting on Gross' departure outside of a brief statement confirming the move.
Gross has a connection to Janus through its CEO, Dick Weill, the former chief operating officer at Pimco.
In terms of assets, Pimco, with $1.97 trillion under management, dwarfs Janus, which has $177.7 billion.
"I look forward to returning my full focus to the fixed income markets and investing, giving up many of the complexities that go with managing a large, complicated organization," Gross said in a statement. "I chose Janus as my next home because of my longstanding relationship with and respect for CEO Dick Weil and my desire to get back to spending the bulk of my day managing client assets."
Amid a swirl of reports that Gross was forced out, Pimco officials acknowledged internal tensions between Gross and the board.
"While we are grateful for everything Bill contributed to building our firm and delivering value to PIMCO's clients, over the course of this year it became increasingly clear that the firm's leadership and Bill have fundamental differences about how to take Pimco forward," CEO Douglas Hodge said in a statement.
Read More'Mediocre' Gross overpaid at $200 million: Trustee
Pimco promised there would be no leadership void, citing a succession plan it has in place that would select from "a deep bench of talent with extensive investment and leadership experience" to succeed Gross.
The move comes amid news that the Securities and Exchange Commission is investigating whether Pimco inflated the value of its primary exchange-traded fund, the $3.6 billion Pimco Total Return. The probe, which sources told the Wall Street Journal has been ongoing for a year, is focusing on how the firm bought and then valued assets in the fund.
Pimco has denied any wrongdoing.
The ETF was off only slightly but was trading at record volume levels.
Pimco itself has hard a difficult year, losing favor with clients who have been pulling their money at a fairly sharp pace. Its flagship Total Return mutual fund has suffered through a string of monthly outflows, knocking its value down more than $40 billion to $221.6 billion, with about $25 billion in outflows for 2014 alone, according to Morningstar. The fund is up 3.29 percent year to date, trailing the benchmark Barclays U.S. Aggregate Bond index, which is up 4.19 percent.
The Total Return ETF has seen outflows of about $71 million for the year.
Read MorePimco flagship fund is still bleeding billions
Gross also has taken his lumps. He was the subject of an unflattering Journal feature earlier this year that portrayed him as autocratic and difficult to get along with.
That story came on the heels of the high-profile departure of former Pimco CEO Mohamed El-Erian, who is now chief economic adviser for Allianz. Reports focused on tension between longtime cohorts Gross and El-Erian, with the former receiving the bulk of the bad press.
Read MoreGross on Pimco: Better 'than we were before'
"There have been a lot of people who have been kind of wiggly and anxiety-ridden ever since the Mohamed El-Erian debacle," said Marilyn Cohen, head of fixed income money manager Envision Capital Management in Los Angeles. "Their performance has been kind of so-so. I think this is going to be a catalyst for more money leaking out of Pimco."
—CNBC's David Faber contributed to this report