More than 600 US-based Cambodian convicts have been forcibly returned to the Southeast Asian country since 2002.
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Many were war refugees who were raised in the states and now arrive as strangers in their homeland, severed from relatives in the US and unable to speak the local language.
Cambodia said last year it wanted to rewrite the agreement, which it criticised as a "double punishment" for deportees who are shipped back after serving sentences in US jails.
In protest of the arrangement, Cambodia delayed processing paperwork for returnees for several months.
But it began cooperating again after the US retaliated by levying visa sanctions against senior foreign ministry officials in September.
The new arrivals landed at Phnom Penh's airport on Thursday morning and were whisked away in police vans to an immigration department, a senior immigration official told AFP, requesting anonymity.
"They arrived at 7:45 am this morning," he said.
Later on most were taken to an NGO that helps provide housing and job support for deportees, known colloquially as "Khmericans", in Phnom Penh.
The group, which is the largest to arrive in one batch in 15 years, were flown in from the US in shackles, said Bill Herod, an American who works with the Khmer Vulnerability Aid Organisation (KVAO).
"It's been an unbelievably difficult experience (for the group)," he told AFP, slamming the repatriation policy as "unjust and unfair".
"These people don't have any real connection to Cambodia. Their parents are from Cambodia but they are Americans socially, they eat American food, they listen to American music."
Most of the Khmericans were newborns and toddlers when their families fled the Khmer Rouge, which killed or starved to death nearly a quarter of Cambodia's population in the late 1970s.
It wasn't until 1996, years after they arrived as refugees in America, that the US passed laws mandating the deportation of greencard-holders convicted of felonies.
Some are swooped up years after they have been released from prison and returned to normal life.
Over the past year US authorities have ramped up immigration raids under President Donald Trump, whose administration has taken a hardline stance on expelling criminals and undocumented migrants.
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