The New York Times first reported that Hicks would resign and sources with knowledge of the matter confirmed she would be leaving to ABC News.
After the news broke, Trump said he "will miss having her by my side."
"Hope is outstanding and has done great work for the last three years. She is as smart and thoughtful as they come, a truly great person," the president said in a statement provided to the media by White House press secretary Sarah Sanders.
"I will miss having her by my side but when she approached me about pursuing other opportunities, I totally understood. I am sure we will work together again in the future," Trump said.
In her own statement, also provided by the White House, Hicks said: "There are no words to adequately express my gratitude to President Trump. I wish the President and his administration the very best as he continues to lead our country."
Hicks delivered a tearful goodbye to her staff Wednesday afternoon, saying she's decided to leave because she doesn't like Washington and doesn't want to be part of the system, a source in the room told ABC News.
According to this source, Hicks also did not rule out the possibility that she could later return to the administration in some capacity. "She may be back," the person said. "She loves this president."
Speaking to reporters earlier, Sanders said Hicks was not resigning because of her testimony Tuesday before the House Intelligence Committee during which she said she had occasionally told white lies on Trump's behalf, according to a source familiar with the interview.
“This is something she’s been thinking about for a while,” Sanders said, adding that Hicks was going to spend some time with her family.
"Quit trying to make it into a scandal. Don’t try to read more into it than there is,” Sanders told reporters.
Hicks's comments during the nine-hour House committee interview were first reported by The New York Times.
“When specifically asked whether or not she was instructed to lie by the president, or the candidate, with regard to Russia, the investigation or our investigation, the answer to that question was no,” Rep. Tom Rooney, R-Fla., told The Associated Press. “And that’s our jurisdiction. Not whether or not he asked her to cancel a meeting for him, or something like that.”
Manafort pleaded not guilty Wednesday to charges including bank fraud and tax evasion brought as part of special counsel Robert Mueller’s investigation into Russian meddling in the 2016 presidential election.
ABC News' Cecilia Vega and Jordyn Phelps contributed to this report.