The Boro midfielder is set to depart for his native Argentina on a season long loan.
Boca will also hold an option to buy the player following the conclusion of the campaign.
Payero signed for Boro last summer in a £6 million deal, but failed to settle in the side under Neil Warnock and Chris Wilder.
The 23-year old started just six games from 13 appearances in the Championship last season as the side finished 7th in the league.
Payero still has two years remaining on his contract with Boro, but it is becoming increasingly likely that his time at the Riverside is coming to an end.
Middlesbrough had interest from multiple clubs, including the player’s former side Banfield, before eventually coming to an agreement with the Argentine giants.
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This will spell the end of a difficult period for the midfielder as he looks to get back up to full match fitness in order to try and play his way in the Argentina World Cup squad for this winter.
Meanwhile, Boro will be planning for life in the second division without the player, with their opening game coming against West Brom on July 30.
This is a move that had a lot of promise 12 months ago but has absolutely fizzled out.
Moving Payero on is the best move now for all parties involved.
The hope will be that he can perform back in his native Argentina and that Boca will take up the offer to buy at the end of the season.
Otherwise, Boro could end up in this situation again in a year, with a player on their books that is not set to be part of the first team plans.