AFP Sport highlights five challenges facing the 63-year-old as he returns to the team he coached from 2012 to 2015.
Rediscover winning habit
Jones is one of the most respected coaches in rugby but his recent record has prompted critics to suggest he has lost his magic touch.
Having taken England to the World Cup final in 2019, he led them to their worst season in more than a decade in 2022, winning five of 12 Tests that year and getting the sack.
His record as Australia head coach was even worse. The Wallabies won two of their nine games including a worst-ever World Cup where they failed to make it out of the pool phase.
Jones's first game in charge of Japan could be a home Test in Tokyo against England in June.
The arch mischief-maker would love nothing more than to get back to winning ways at his former employer's expense.
- Make friends -
Jones is still revered in Japan for his first stint in charge, when he led the Brave Blossoms to a historic win over South Africa at the 2015 World Cup.
But he also had his naysayers in a country with powerful rugby factions that do not always see eye to eye.
Jones cut a prickly figure during his abortive second spell with Australia, telling reporters to "go give yourselves uppercuts" when they questioned his World Cup squad selection.
Such a combative approach rarely goes down well in Japan and he will need to refind the genial twinkle in his eye that characterised his first stint as Japan boss.
Uncover new talent
Jones's predecessor Jamie Joseph was loyal to several veterans who may not be around for the next World Cup in 2027.
Michael Leitch, Keita Inagaki and Pieter Labuschagne are all in their mid-30s, while full-back Kotaro Matsushima is 30 and captain Kazuki Himeno 29.
Joseph did uncover some young talent, with lock Warner Dearns, centre Tomoki Osada and fly half Lee Seung-sin all 23 or under and looking like mainstays for the future.
Jones was pilloried for replacing Australia's veterans with rookies but his faith in youth could stand him in good stead in Japan.
Make the most of big games
Japan have long been hampered by a lack of regular games against the world's top teams but that will change if they are included in a new biennial competition starting from 2026.
The Brave Blossoms and Fiji are expected to be invited to join sides from the Six Nations and southern hemisphere's Rugby Championship for the 12-team tournament.
That will be a step forward but it will still give Jones fewer opportunities to work with his players than he was used to with England and Australia.
He will have to make do with Pacific Nations Cup matches against fellow tier-two teams until the new tournament kicks off.
Survey league landscape
Joseph was adamant that the Sunwolves, the Tokyo-based team that competed in Super Rugby from 2016 to 2020, were crucial in preparing his players for the 2019 World Cup, where they reached the quarter-finals on home soil.
The New Zealander was not so keen on Japan Rugby League One, the domestic competition that has made headlines by signing star players from around the world.
The Japanese league signed more big names for this season, with a host of All Blacks and Springboks taking centre stage.
How that affects the national team is something for Jones to think about.
