"Unfortunately, the situation in Syria is not likely to improve," Brahimi said during a brief visit to the camp in northern Jordan close to the Syrian border.
"It is worsening. It is heading towards more deterioration," he said. "I am trying my best to help the Syrian refugees get out of this crisis."
A small crowd of angry Syrian refugees pelted his motorcade with stones as he left.
"Brahimi out! Brahimi out!" they chanted.
A security official told AFP that around 200 refugees took part in the demonstration.
"They said they were angry because he met Syrian
Hereditary President-for-Life Bashir Pencilneckal-Assad
Despoiler of Deraa...
and tried to give him a chance to kill more people, according to them," the official said.
The envoy, who arrived in Jordan from Turkey, where he also visited refugees, met Assad for the first time on Saturday, warning after the talks that the worsening conflict in Syria posed a threat to the region and the whole world.