Reuters reported that at least three people were killed and 20 others were wounded in the incident at the Rukban camp.
According to the Jerusalem Post, the checkpoint is manned by the Jaish al-Ashair rebel group.
Hala Akhbar, a website linked to Jordan's military, also reported the blast, according to the Washington Post.
A rebel official said that Daesh was suspected in the attack.
The camp is home to around 75,000 people displaced by fighting in the region.
Following a June car bombing that left seven border guards dead, Jordan closed off the border with Syria, cutting off aid to thousands of Syrians in the area.
