"I've had doubts but finally decided that I had to take this step," Van Marwijk, who last year extended his contract by four years until 2016, said in a statement on the Dutch FA's website
The Dutch, World Cup finalists in 2010, exited the European Championship in Poland and Ukraine having lost all three group games, their worst performance at a major tournament.
A 1-0 opening defeat by Denmark was followed by 2-1 defeats against Germany and Portugal.
Dutch media and fans blamed Van Marjwik for the team's failure, criticising him for being too conservative, but several players offered their support.
"Van Marwijk did an extremely good job with guiding the team to the final of the 2010 World Cup and first place in the FIFA rankings," said KNVB director Bert van Oostveen.
"It is sad that we have to say goodbye right now but we also have to be realistic."
Van Marwijk, 60, took charge of the national side in July 2008 after Marco van Basten resigned. Under his guidance, the Dutch won 14 consecutive competitive games before losing 1-0 to Spain in the 2010 World Cup final.
The Dutch were also impressive in Euro 2012 qualifying, winning nine in a row before losing to Sweden in their final qualifier.