Jennifer Pagonis, deputy permanent representative of the UN High Commission for Refugees in Sri Lanka, told Xinhua that 37 people from 15 families returned to Colombo on a commercial ferry.
The refugees left Tuticorin in India's Tamil Nadu state, which is separated from northern Sri Lanka by a strip of sea.
"They are all from the north and east of Sri Lanka. They are being processed by immigration officials and will be sent home," said Pagonis.
The group's arrival is the first repatriation of Sri Lankan refugees in India by sea, the UN agency said.
According to the Indian government, 69,000 Sri Lankan refugees still live in 112 camps in Tamil Nadu.
In May 2009, the long conflict between Sri Lankan forces and the Tamil Tigers ended.
In the final phase of the war, about 276,000 people were displaced, with the many fleeing to India, UNHCR said.
Since then, many Sri Lankans have returned to their homes, but there are still a significant number awaiting repatriation. According to the UNHCR, over 1,400 refugees have returned this year, compared to 2,054 last year.