Cueva will join Chelsea for a 750,000 fee, says the Daily Mail.
"Bernardo has done a fantastic job for us over the last four seasons," said director of football Phil Giles.
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"His first season ended with promotion to the Premier League, and he has played a key role in us now achieving four successive Premier League seasons.
"Part of Bernardo's role relates to our set-piece strategies, and this is an area I think everyone at the club can be proud about.
"He leaves with the blessing and best wishes of everyone at Brentford."
Cueva has acted as the Bees' tactical statistician, with the role including work on their set pieces.