"There have been talks to continue on this road, however, the federation has taken so much time to make a decision for the future, that I felt that it was time for me to move on," the 57-year-old coach posted on Instagram.
Van't Schip's contract with the federation ends on December 31st but he said "at the end our vision on football is different and doesn't align. In order to be able to have success everyone needs to be on the same page."
The federation has yet to comment on van't Schip's decision but Greek media had predicted that after the team failed to qualify for the 2022 World Cup his job would be in jeopardy.
Van't Schip coached the squad for 26 matches with 11 victories, 9 draws and 6 defeats.
The Canadian-born former Dutch international winger was hired for the Greek post in the summer of 2019 after coaching Dutch clubs PEC Zwolle, Ajax, Jong Ajax and Twente as well as Australia's Melbourne City and Melbourne Heart before heading to Guadalajara in Mexico.
He was also assistant to the Netherlands national team from 2004-2008.
Van't Schip played 41 times for the Dutch national team, scoring two goals from 1986 to 1995, and on a club level played for Genoa and Ajax.