He strode across the finish line with his arms crossed over his head in a sign of solidarity for the Oromo people, his native group and the largest ethnic group in Ethiopia. He repeated the sign at a press conference.
In an interview after the race, Lilesa said he wanted to draw attention to the government's ongoing persecution of the Oromos.
By speaking out, he said, he put himself into such danger that he can't go home.
"I really think that I would be killed," he said -- or imprisoned. Some of his family members are already in prison, he said, and he worries about the safety of his wife and two children.
Lilesa said he may stay in Brazil or go to Kenya or the United States, depending on whether he can obtain a visa for those moves.
It's unclear if his gesture with the arms will affect his medal. In the past, the Olympics committee has stripped athletes of their medals for political protests, as when American sprinters Tommie Smith and John Carlos
gave the black power salute on the medal stand at the 1968 games.
The Oromo make up at least a third of Ethiopia's 100 million people
. But they have been marginalized for decades, with tensions rising recently as the government promoted development that took over over Oromo farmland.
Huge protests by the Oromos
have swept the streets of Ethiopia.
The government was brutal in putting down the demonstrations, nonprofit groups like Amnesty International and Human Rights Watch reported.
"In nine months, more than 1,000 people have been killed," Lilesa said on Sunday.
CNN could not immediately confirm this statement. Human Rights Watch
said that since November, more than 400 people have been killed and tens of thousands arrested. Thousands more have been jailed.
"Human Rights Watch's research indicates that security forces repeatedly used lethal force, including live ammunition, to break up many of the 500 reported protests that have occurred since November 2015," the group reported on its website.
In response to the protests and the report from Human Rights Watch, Getachew Reda, Ethiopia's Minister of Communications, told CNN that the country's security response was standard police protocol to disperse "rioters." He also disputed the number of deaths.
Some of the protesters have been armed with guns and hand grenades, he added.
In a report on the Oromos, Amnesty International said
at least 5,000 Oromos were arrested because of peaceful protests or opposition to the government between 2011 and 2014.
Lilesa won silver on Sunday with a time of 2:09:54, finishing behind liud Kipchoge of Kenya. He finished with a time of 2:08:44.