Protesters included North Korean refugees and US Christian activist Robert Park, who two years ago was held by the North for 43 days after he crossed the border to stage a one-man protest over human rights violations.
"Stop genocide!" he shouted after an emotional speech that blasted human rights abuses especially in the North's camps for political prisoners.
According to South Korea's state human rights watchdog, North Korea has six such camps housing about 200,000 in total.
The rally was held to mark International Holocaust Remembrance Day, the 67th anniversary of the liberation of the Nazi death camp at Auschwitz.
Organisers said similar rallies were to be held in Tokyo and other foreign cities.
"We must bring the spring of freedom and democracy to North Koreans," said Ji Seong-Ho, a 31-year-old refugee who has led an anti-Pyongyang group since he arrived in Seoul in 2006.
"It's time to act and let North Koreans know that we and the international community are working for them," he told AFP.
Ji and others issued a statement calling for Seoul to intervene to protect the safety of North Korean refugees in China and accusing Beijing of repatriating some 5,000 such refugees every year.
"Tens of thousands of innocent North Koreans have been killed and innumerable families torn apart as a direct consequence of China's inhumane, illegal and unjustifiable policy towards the North Korean refugees," it said.
After the rally the demonstrators marched to the Chinese consulate to deliver a letter urging Beijing to stop repatriating North Korean refugees.
The letter said many of them face torture, imprisonment or even execution when returned to their homeland.
Rights groups have criticised China's policy of repatriating North Koreans as economic migrants, rather than giving them refugee status.