The 43-year-old guided Excelsior to 15th place in the Dutch league last season and will replace Mark Warburton at the west London Championship (second tier) side.
Warburton led Brentford to fifth in the Championship last season, before they lost 5-1 on aggregate to Middlesbrough in the promotion playoffs, but the club announced in February that he would leave as part of a restructuring process.
"The appointment of the new head coach was a very important part of the restructure of the football management we have been undertaking," owner Matthew Benham told the club's website.
"We wanted someone who could share our vision for the future of Brentford.
"There was a wide search and lots of candidates were considered but Marinus was the overwhelming choice of everyone involved in the selection process."
Benham, who made his fortune by using data and mathematical models as a betting tool, has been keen to increase the use of statistics in the club's player recruitment process.
Former striker Dijkhuizen will be assisted by Roy Hendriksen, who joins from Dutch side NEC Nijmegen, and the pair will work closely with recently appointed co-directors of football Rasmus Ankersen and Phil Giles.
"I am proud to be the new head coach of Brentford," said Dijkhuizen, who had been manager of Excelsior since January 2014.
"I have been to Brentford once before, with my father and brother, to see a game against Coventry City in March 2014.
"We stood on the terrace behind the goal and were pleasantly surprised by the quality of football.
"We also loved the ambiance in and around the stadium."
(Reporting By Michael Hann; Editing by John O'Brien)
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