Clattenburg's departure was confirmed by Professional Game Match Officials Limited (PGMOL), the organisation which provides and trains officials for the Premier League, English Football League and Football Association.
The Saudi Arabian Football Federation announced he was to manage referees in the Middle East country, with Clattenburg saying he wanted to help establish a professional refereeing set-up.
One of the Premier League's leading referees at the time of his exit, Clattenburg had in 2016 taken charge of the European Championship, Champions League and FA Cup finals.
Clattenburg said on the Saudi Arabian Football Federation's Twitter page: "This is an important move forward. We have professional referees in the country that I am leaving, which has been a big positive. One thing I'd like to do is work with the refereeing team and the president to make this happen so that it will be successful for many, many years to come."
The Durham-born official oversaw his first Football League game as a 25-year-old in 2000, was promoted to PGMOL's Select Group in 2004, and became a FIFA referee in 2006. His list of notable matches includes the men's football final at the London 2012 Olympics.
In 2008 and 2009, Clattenburg served an eight-month suspension after PGMOL investigated his business dealings.
In 2012 Chelsea made a formal complaint that he had used inappropriate language towards Jon Obi Mikel during a game against Manchester United – he was subsequently cleared of any wrongdoing.
Clattenburg was then reprimanded by PGMOL boss Mike Riley in 2014 for breaches of protocol when he drove to Newcastle to see an Ed Sheeran concert after refereeing a Crystal Palace versus West Brom game and spoke to Neil Warnock, Palace's manager at the time, on the phone.
His last Premier League match prior to the news that he was to depart for Saudia Arabia was Arsenal's 2-0 home win over Hull five days earlier, which saw controversy over an Alexis Sanchez goal that went in off the Chilean's hand, and the decision to give Kieran Gibbs a yellow card rather than a red for a foul on Lazar Markovic.
PGMOL said in a statement: "The Professional Game Match Officials Limited would like to wish Mark Clattenburg well as he prepares for his move to the Saudi Arabian Football Federation. Since joining the PGMOL Select Group in 2004, Mark developed into one of our top officials, refereeing at the highest level and setting standards for others to follow.
"Mark is a talented referee, he has been a great asset to the English game and hopefully an inspiration to those who want to get into refereeing at the grass roots of the game. We understand this is an exciting opportunity for Mark as well as further underlining what high esteem English match officials are held throughout the world game."
Clattenburg replaced former Premier League referee Howard Webb in the role in Saudi Arabia, and held the post until October 2018.