"F-16 fighter jets from the royal air force downed a drone near the northern border with Syria," an air force official said, reading from a statement.
Air force staff were gathering the debris of the aircraft in the northern province of Mafraq to analyse them, he said.
Jordan shot down an identified a drone in Mafraq in 2014.
The kingdom, which shares a desert border of more than 370 kilometres (230 miles) with Syria, is part of the US-led coalition fighting the Islamic State militant group in Syria and Iraq.
On Tuesday, Syrian regime forces and US-backed rebel fighters clashed in a remote desert area near the Jordanian border where the rebel group shelters families of its fighters.
"The Syrian regime's jets conducted four strikes against us," Tlas al-Salameh, the commander of Osoud al-Sharqiya [Eastern Lions] said at the time.
Eastern Lions is a Western-backed Free Syrian Army (FSA) faction, which is the largest operating in the Syrian Desert bordering Jordan.
The group suffered no casualties in the airstrike, Salameh said, accusing government troops of "obstructing" his group's efforts against Islamic State group militants.
"The regime forces have entered the area and blocked the way between us and Daesh," Salameh said, using an Arabic acronym to refer to IS. "We can't get to Daesh."
Others hit a rebel outpost eight kilometres from the Rukban camp, where more than 80,000 refugees are stranded on the Syrian-Jordanian border.
The clashes came two days after Syrian media said the US, UK and Jordanian forces were "massing" on the Jordanian side of the border. The report was likely a reference to the annual US-Jordanian military drill Eager Lion.
Jordan's state-run Petra news agency said about 7,400 troops from more than 20 nations were participating.
On Monday, Syria's Foreign Minister Walid al-Muallem warned Jordan against sending troops to Syria, adding that the government troops' next target would likely be to reach the border with Iraq.
A six-year war in Syria has killed more than 320,000 people and displaced millions.
The UN refugee agency says it has registered more than 650,000 Syrian refugees in Jordan since the war broke out in 2011. Amman says it hosts 1.3 million Syrian refugees.
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