General Joseph Votel, head of US Central Command (Centcom), met US military advisors working with Syrian Arab fighters, a Centcom spokesman said.
He also met leaders of the Syrian Democratic Forces (SDF), the spokesman said, without providing further details.
During the secret trip, which lasted several hours, the Centcom commander visited a handful of locations, CNN reported as it accompanied Votel, the highest-ranking US military official to travel to Syria since its civil conflict began in 2011.
US special operations forces are helping train fighters in Syria to combat the IS group as Washington leads a coalition of countries in an air war against the jihadists in Iraq and Syria.
The IS group has seized swathes of territory in Syria and Iraq to create a self-styled "caliphate." Its leader, Abu Bakr al-Baghdadi, has received pledges of allegiance from jihadist groups around the world.
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The United States has roughly 200 advisers on the ground in Syria, but no combat units. Votel's visit comes as the first of 250 more US special operations forces are beginning to arrive.
Kurds play a dominant role in the US-backed SDF, providing the core of the forces that have pushed back the IS group group in the country's northeast.
The SDF has a total of about 25,000 Kurdish fighters and about 5,000 Arab fighters.
Washington is pushing to bring more Arab forces into the group.
The Syrian war erupted in early 2011 after Assad's forces launched a brutal crackdown on anti-government protests, and has since claimed more than 270,000 lives.
Votel's visit comes after international talks on ending the Syrian conflict broke up with no clear breakthrough earlier this week as new faction-fighting erupted and the death toll continued to mount.