The report included stories of fathers deported without being given a chance to tell the families they leave behind.
It said a 12-year-old boy was left without money at the border, forced to beg for bus fare to Afghanistan.
Millions of Afghans fled to Iran and Pakistan in the 1980s to flee a bloody anti-Communist insurgency. At the peak of the war, roughly 5 million refugees lived in Pakistan and nearly 4 million in Iran.
But Iran has refused to register many of them, said Faraz Sanei, Human Rights Watch researcher for Middle East and North Africa. Roughly another 840,000 Afghans live in Iran as registered refugees.
More From This Section
Senei said the report's authors spent more than one year on Afghanistan's western border with Iran interviewing refugees as they straggled across the border, some telling horrific tales of being beaten and abused.
"The most serious concerns that we have are the many undocumented Afghans in Iran who, when they are deported, go through some very very serious abuses during the deportation process," Senei told reporters in the Afghan capital.
"As the Iranian government ratchets up the pressure on Afghans to leave, Afghanistan's deteriorating economic and security situation increases the dangers for returnees," he said.
The report urged Iran to set up reception centers for unaccompanied children, provide greater assistance to deported Afghans, and end the abuses of Afghan refugees and migrants.