Ellis is quitting just weeks after leading USA to a successful defence of the World Cup title, U.S. Soccer announced.
She plans to stay with the national team for their five-game victory tour, which starts on Saturday against the Republic of Ireland at the Rose Bowl in Pasadena, California, and will end in early October.
"The opportunity to coach this team and work with these amazing women has been the honour of a lifetime," Ellis said in a statement.
"I want to thank and praise them for their commitment and passion to not only win championships but also raise the profile of this sport globally while being an inspiration to those who will follow them.
"When I accepted the head coaching position this was the time frame I envisioned. The timing is right to move on, and the programme is positioned to remain at the pinnacle of women's soccer.
"Change is something I have always embraced in my life, and for me and my family this is the right moment."
The move comes as no great surprise, with Ellis' contract expiring on Wednesday, though there was an option to extend her stay through next year's Olympic Games in Tokyo.
While this is the end of her USWNT coaching career, Ellis will continue to work with the federation for at least the next year in the role of an ambassador, representing U.S. Soccer at various events.
The 52 year-old became the eighth head coach of the national team when she took over in 2014 after serving two separate stints as interim coach. She replaced Tom Sermanni after his dismissal.