Football Association of Thailand (FAT) president Pol Gen Somyot Poompunmuang announced his resignation on Saturday over a 2023 SEA Games fiasco which saw the country's U22 team lose to Indonesia in the final.
Somyot had also courted criticism for a brawl during the title showdown involving players and officials from both teams.
Indonesia trounced Thailand 5-2 in extra time in the May final that saw players and coaches on both sides clash on two occasions with four red cards issued.
Thailand's football association later apologised and handed out lengthy bans to two players, two officials and a coach.
On Friday, Thai Olympic chief Gen Prawit Wongsuwon said Somyot should take responsibility for the U22 team's failure to win the gold medal at the 32nd SEA Games final and a brawl that marred the men's final in Cambodia.
Speaking during an annual meeting of the National Olympic Committee of Thailand (NOCT), Prawit said the brawl had damaged the reputation of Thailand.
"I said before the SEA Games that if the team didn't get the gold medal, the football chief should step down," said Prawit. "So now I ask if he would take responsibility and quit his post?
"And then there was a brawl during the final against Indonesia, which wasn't the first time for our national football team. I find this is unacceptable."
In a statement on Saturday, Somyot said Thai deputy prime minister Prawit had ordered him to stand down as president at a meeting on Friday.
"As President of the Football Association of Thailand... I am ready to follow the order of General Prawit," Somyot said in Saturday's statement.
He added that he would notify the Asean Football Federation (AFF), the Asian Football Confederation (AFC) and the international governing body Fifa about the development and the reason behind his resignation.
The final had been billed as a chance for Indonesia to restore some pride to its football following a deadly stadium disaster and the loss of rights to host the U20 World Cup.
But the game will be remembered for the chaotic scenes which began in the 97th minute when Thailand -- who at one point had been 2-0 down -- scored to make it 2-2 and force extra time.
Thai officials celebrated by running over to the Indonesia bench, prompting the first melee, and there was more trouble when Indonesia retook the upper hand early in extra time. Bangkok Post/AFP