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New Zealand Rugby formed a partnership with Harlequins in 2018.
The club's head of rugby Paul Gustard said: "It is not common practice for this to occur, which we accept, but we are not a normal club and must have both Joe's and the club's best interests at heart.
"I believe his genuine desire to play Super Rugby was so great that we wanted to make sure he had this opportunity."
Blues coach Leon MacDonald said his players would benefit as much as Marchant from the move.
MacDonald said: "New Zealand has developed innovative ways to retain and invigorate our best talent, and sabbatical clauses have become one of those tools to retain our best talent long-term.
"It's fantastic to be part of a similar arrangement in reverse for such a promising young English player.
"Joe has impressed us on and off the field and we look forward to him joining us in January. We are confident that he will learn from his experience in Super Rugby and certainly our players, especially our young backs, will greatly appreciate learning from him."
Blues back Harry Plummer and high performance manager Tony Hanks have spent time with Harlequins.
Marchant has played for England under-18/20s, and 85 games for Harlequins. He played for England in a World Cup warm-up match against Italy.
Marchant said: "I am exceptionally thankful to Gussy and the management for helping give me the chance to test myself in a league I have always wanted to play in whilst I am in my prime.
"I am really excited to be given the chance to experience playing in Super Rugby. I am sure that I will learn a lot and I can't wait to bring my learnings back to the Club."
The Blues have been hit by departures with SBW heading to the Toronto league club, Nonu joining the San Diego team, Clarke being part of the sevens programme and Nanai signing for Worcester Warriors. Former Hurricane Barrett's position is unclear under his new, flexible national contract.