The decision will give Defense Secretary Jim Mattis the authority to send more forces into Syria, to assist US-backed local troops as they move to retake Raqqa from the Islamic State group, which has used the city as a de facto capital.
It will also let him adjust the force numbers in Iraq, in the ongoing fight to oust IS from Mosul and stabilize it as the rebuilding begins.
Those moves were done with White House approval, but without any formal adjustment to the longstanding troop caps that had been set by the Obama administration.
Dana White, chief spokesperson for the Pentagon, said Wednesday that Mattis has not made any changes yet to the current authorised force levels.
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Under the Obama White House, military leaders chafed about micromanagement that forced commanders to get approvals for routine tactical decisions and personnel moves, and provide justification for any troops sent into war zones.
The new authority will provide greater transparency about the actual number of US forces in Iraq and Syria after several years of public confusion about the accurate totals.
Under the Obama-mandated caps, the US was limited to 503 officially deployed troops in Syria, and 5,262 in Iraq. The Pentagon, however, has closer to 7,000 in Iraq, and hundreds more than the cap in Syria, but doesn't count them because they are on temporary duty or not counted under specific personnel rules.
Officials worry that if they publicly acknowledge there are thousands more troops there, it could fuel opposition and problems for the Iraqi government.
Trump's decision applies only to the two countries, and so far does not affect Afghanistan, although that change has also been discussed.
"This does not represent a change in our mission in Iraq and Syria to defeat ISIS," said White, using another name for the Islamic State group.
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