In one of the most emotional moments of his trip to Japan, Trump met the now elderly families of those abducted, who were clutching pictures of their loved ones.
The issue sours already strained Japan-North Korea relations and Prime Minister Shinzo Abe often wears a blue ribbon to remind him of their abduction.
Among those the president met was the ageing mother of Megumi Yokota, who was 13 when kidnapped four decades ago on her way home from school.
"We heard the very sad stories," said Trump, who took more than half an hour out of his schedule to listen to the families.
"We will work with Prime Minister Abe on trying to get them back to their loved ones," he added.
Following the meeting, which was closed to the press, the family members stood side by side with Trump and Abe, holding photographs of their loved ones, for a photo session.
Trump shock hands with some of them as he left the room.
Afterwards, Trump appeared to hold out some sort of deal to North Korea's bellicose young leader Kim Jong-Un over the abductees.
"I think it would be a tremendous signal if Kim Jong-Un would send them back," he told reporters as he stood with Abe after meeting the family members.
"If he would send them back, that would be the start of something very special, if they would do that," Trump said.
Takuya Yokota, a brother of Megumi, said Trump was shaking his head when he looked at a picture from the happy days of the Yokota family.
"I had the impression that the president knows this issue well and has sympathy for us," he said.
"I was feeling tense but the president shook hands with every one of us gently," said Hitomi Soga, who was kidnapped in 1978 along with her mother but was allowed to return in 2002.
Shigeo Iizuka, brother of Yaeko Taguchi, said the meeting with Trump could be "a stepping stone for us to move forward".
In 2002 North Korea admitted kidnapping 13 Japanese civilians but the government in Tokyo believes at least 17 were taken.
A month later, five were allowed to return to Japan. Pyongyang insists the other eight are dead but has not produced cast-iron evidence.
"No child should ever be subjected to such cruelty. No parent should ever have to endure heartbreak," said Trump.
Megumi Yokota was among those said to have died and in 2004 North Korea handed over cremated remains it claimed were hers.
However, Tokyo said DNA tests conducted in Japan proved the claim to be untrue.
There are strong suspicions in Japan that dozens of other citizens were also snatched by the North.