He follows his boss Defence Secretary James Mattis out of the Department of Defence after he resigned last month in protest at the move and his decision to halve troop numbers in Afghanistan.
Rear Admiral Sweeney, according to The National said in a statement that “the time is right to return to the private sector”. He was in the post for two years and called it an “honour to serve” in the position. Department spokeswoman Dana White also resigned after the Syria announcement.
Trump has faced criticism for his decision to withdraw from Syria over fears that ISIS or Iran will fill the vacuum left by US troops.
While the president appeared to suggest a rapid withdrawal, the pace of the American exit has appeared to have slowed, with officials briefing that the US is not going anywhere and that any withdrawal of some troops would be managed carefully.
Mattis criticised the president upon leaving office, writing a letter that talked about “treating allies with respect” after the perceived betrayal of Kurdish allies in northern Syria.
Trump said on Friday a New York Times report that he was considering former Democratic Senator Jim Webb to be his next defence secretary was “fake news”.