Zichal, 37, plans to leave by year's end, the White House said. It did not say where she would be going or who would replace her.
Obama released a statement Friday describing Zichal as a "trusted adviser."
"Heather has overseen some of our biggest achievements in energy and climate change, including establishing historic new fuel economy standards that save consumers money, reducing mercury pollution from power plants to keep our kids safe, supporting the growth of homegrown clean energy that creates good new jobs, and enacting my Climate Action Plan that will help us leave a safer planet for our children," he said. "Above all, Heather's efforts have proven that strengthening America's energy security does not have to be a choice between economic growth or good environmental stewardship -- it can mean both."
The Washington Post said Obama personally appealed to Zichal to stay.
Dan Utech, Zichal's deputy, was mentioned as a candidate to replace Zichal, Politico said.
Other names Politico cited include Kevin Knobloch, chief of staff to Energy Secretary Ernest Moniz and previously the head of the Union of Concerned Scientists; Gary Guzy, deputy director of the Council on Environmental Quality and an Environmental Protection Agency general counsel from the Clinton administration; and Frances Beinecke, president of the Natural Resources Defense Council.
Zichal has been deputy assistant to the president for energy and climate change since January 2009 and gained the general responsibility of coordinating the administration's energy and climate policy in March 2011 after the departure of climate czar Carol Browner.
During her tenure Zichal coordinated the work of multiple agencies on issues ranging from air quality to global warming. She was key in pushing for stricter fuel-efficiency standards for cars and limits on mercury and other toxic emissions from power plants, the Post said.