MUSCAT, OMAN—The top U.S. commander in the Middle East said he is moving forward with plans to pull American forces out of Syria, but said the military has the flexibility to leave some troops there if President Trump decides to maintain an American presence in Syria as a counter to Iran.

Gen. Joseph Votel, head of U.S. Central Command, said equipment is being moved out of Syria as part of Mr. Trump’s plan to withdraw all troops from the country. In the coming weeks, service members also will begin to leave, he said.