A statement from the Syria Democratic Forces (SDF) warned of a military vacuum that would leave the alliance trapped between “hostile parties”.
Mr Trump made the announcement on Wednesday, saying IS had been defeated.
However, major allies and some US politicians have disputed the claim.
A US partnership with the SDF – an alliance of Syrian Kurdish and Arab fighters – is credited with playing a major role in the virtual elimination of IS after it overran large swathes of Syria four years ago.
About 2,000 US troops have largely been stationed in the Kurdish region in northern Syria.
The SDF statement warned that the withdrawal would “negatively impact” the anti-IS campaign and allow the group “to revive itself again”.
It said the US move would have “dangerous implications” for regional stability and “create a political and military vacuum… leaving its people between the claws of hostile parties”.
Neighbouring Turkey has said it is poised to launch a military operation against the Kurdish YPG militia – the main fighting force in the SDF – which it regards as a terrorist group.
US support for the group has strained relations between Washington and Ankara.
The Pentagon said it was transitioning to the “next phase of the campaign” to eliminate IS but did not provide further details.
President Trump, who has long pledged to pull troops out of Syria, said on Twitter that it was time to bring them home after their “historic victories”.
The White House would not give a timescale for the withdrawal but defence officials quoted by the New York Times said President Trump wanted it done within 30 days.
Republican Senator Lindsey Graham, who is one of Mr Trump’s supporters and sits on the armed services committee, called the withdrawal decision a “huge Obama-like mistake”, which would have “devastating consequences” both in Syria and beyond.
He said he feared it would mean ceding influence in the region to Russia and Iran.
Mr Trump’s announcement came only a week after Brett McGurk, special presidential envoy for the global coalition to defeat IS, cautioned again a US withdrawal from Syria.
“Obviously, it would be reckless if we were just to say, well, the physical caliphate is defeated, so we can just leave now. I think anyone who’s looked at a conflict like this would agree with that,” he told reporters at the state department.
The UK government distanced itself from President Trump’s assertion that IS had been defeated.
“Much remains to be done and we must not lose sight of the threat they pose,” a Foreign Office statement said.
French Defence Minister Florence Parly said on Twitter that IS had been weakened but not “wiped from the map”.
“It is necessary that the last pockets of this terrorist organisation be definitively defeated militarily,” she added.
Israel said it had been told the US had “other ways to have influence in the area” but it would “study the timeline [of the withdrawal], how it will be done and of course the implications for us”.
Striking a different tone, Russian foreign ministry spokeswoman Maria Zakharova said the US decision could result in “genuine, real prospects for a political settlement” in Syria.
