According to Sky Sports, the two Championship clubs have settled a figure of £6m.
Jota joined Brentford from Celta Vigo in 2014, but returned to Spain on loan with Eibar for part of the following campaign.
He was at Eibar again during the first half of last season, returning midway through the campaign to return to the Bees. Jota then proceeded to enjoy an impressive run of form, scoring 12 times in his 23 league appearances in the final months of the season.
With Harry Redknapp in charge, Birmingham have been unsurprisingly busy this summer, bringing in 10 players on permanent or loan deals already - including the likes of Craig Gardner, Carl Jenkinson and Jeremie Boga.