"Jordanian authorities have severely restricted" the movement since March of refugees fleeing the war in Syria, the watchdog said in a statement.
The group said it had analyzed satellite imagery that showed large build-ups of refugees stranded just inside Jordanian territory after informal border crossings were shut.
HRW said those trapped "have only limited access to food, water, and medical assistance."
"Jordan should allow the stranded people to move further into Jordan, and let UNHCR, the UN refugee agency, register them as asylum seekers," the New York-based rights group said.
Jordan kept all border crossings with Syria open until mid-2013, after which it began to impose limits on the number of crossing points and the amount of refugees it allowed to enter, HRW said.
"Jordan has gone to great lengths to meet the needs of the Syrian refugees," said Nadim Houry, the group's deputy Middle East and North Africa director.
"But that is no excuse to abandon newer arrivals in remote border areas for weeks without effective protection and regular aid access."
Some 600,000 Syrian refugees have registered with the UN in Jordan, which says it is hosting up to 1.5 million Syrians informally.