The men were put to death by lethal injection in Kunming, Yunnan province.
CCTV News broadcast live footage of the men being taken from their cells to the execution site, though it did not show the moment of death.
Many social media users in China have reacted angrily, condemning the broadcast as insensitive.
It is believed to be the first time in China’s recent history that live footage of condemned criminals being taken to their execution has been broadcast.
Chinese internet users spoke out against the special programme, in what some are saying was a throw-back to the execution rallies of China’s past.
Among the prisoners was Naw Kham, a Burmese man thought to have been one of the most powerful warlords in the Golden Triangle of Thailand, Laos and Burma.
China’s state television channel CCTV aired an interview with Naw Kham on Thursday.
“I couldn’t sleep properly over last two days. I miss my mother. It is really painful that I can’t be with my children,” Naw Kham told the channel.
“My mum didn’t know when I was arrested, and I am worrying that she won’t be able to take it when she finds out,” he went on.
Announcing the execution on Twitter, state news agency Xinhua tweeted a photograph of Naw Kham with his hands clasped in front of his forehead. It is unclear when this picture was taken.
Xinhua has said the men had had their “legal rights fully respected” while on death row.
China’s foreign ministry said the case highlighted its determination to tackle cross-border crime.
“I think an important message that this case sends is that it shows the determination of China and the governments of relevant countries to work hard together to combat cross-border crime,” Hua Chunying spokesman for China’s foreign ministry said.
The 13 fishermen were found dead inside two Chinese cargo ships in October 2011 on the Thai side of the river.
State media said Naw Kham and his subordinates had collaborated with Thai soldiers in launching an attack on the ships, the Hua Ping and Yu Xing.
The other men were Hsang Kham from Thailand, Yi Lai, who is stateless, and Zha Xika from Laos, said the Xinhua news agency.
The group were arrested in Laos and brought to China in May last year, after Beijing said the attack had happened on board Chinese-flagged ships.
Beijing argued that the men should be extradited for trial – a move which some observers saw as an indication of the considerable political and economic clout China now exercises over its smaller neighbors.
In November, the men were found guilty of intentional homicide, drug trafficking, kidnapping and hijacking.
Two other members of the gang were also convicted – one received a death sentence with reprieve and the other eight years in prison.
Thailand launched an investigation into the allegations against nine of its soldiers in connection with the incident.
The attack came amid a wave of hijacking of vessels sailing on the Mekong which were blamed on gangs operating in the notorious drug-trafficking region.
China, Burma, Laos and Thailand launched joint security patrols on the Mekong in response.
Li Zhuqun, a senior international co-operation official at China’s Ministry of Public Security said the gang had now been broken up, but that “efforts to ensure the safety of the Mekong River will continue”.
“We will continue patrols and law enforcement co-operation with the other three countries to safeguard shipping on the river,” he told China Daily.
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