"When I accepted the head coaching position this was the timeframe I envisioned," Ellis said. "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."
Ellis, 52, was appointed in May 2014 and has compiled an overall record of 102 victories, 18 draws and seven defeats.
"The opportunity to coach this team and work with these amazing women has been the honour of a lifetime," Ellis said.
"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."
US Soccer is expected to name a new women's national team general manager soon who will be instrumental in selecting Ellis's replacement.
"The US Soccer Federation and the sport in general owes Jill a debt of gratitude," said US Soccer president Carlos Cordeiro.
"Jill was always extremely passionate about this team, analytical, tremendously focused and not afraid to make tough decisions while giving her players the freedom to play to their strengths.
"She helped raise the bar for women's soccer in the USA and the world and given the history of this programme, the level of success she achieved is even more remarkable."