The 53-year-old will return to his native Holland to contribute to the palliative care of his Father.
Michael Valkanis has been appointed interim first team coach with immediate effect while the Club conducts a search for a permanent replacement for van’t Schip.
Commenting on his decision van’t Schip said: “I have been faced with a choice between my family in Holland and my work here in Australia and there was only one right decision. I did not want my personal circumstances to impact the Club in any way.
“I am part of a strong coaching team that has been carefully nurtured over the last three years and that gives me great confidence that this situation will not adversely affect the Club’s progress.
“I would like to thank everyone at Melbourne City and the City Football Group for their support. The Club’s development since its creation will always be a source of great personal pride to me.”
Reacting to the news. Chairman of Melbourne City FC, and the City Football Group, Khaldoon Al Mubarak said, “John’s reaction to his personal circumstances is testament to the man he is and why he has been such an important contributor to the Club’s development both on and off the field – culminating in guiding our Men’s First team to its maiden trophy. He has our ongoing gratitude and support as his focus rightly turns to his family.”