Mr Charupong, a former interior minister, remains in hiding and faces an arest warrant for failing to repoprt to the National Council for Peace and Order (NCPO).
In a letter to the party, he said he wanted his resignation to be effective from May 22, the day of the military coup. The letter was received on Monday, said Chavalit Wichayasut, acting deputy secretary-general of Pheu Thai.
Mr Chavalit said on Friday that the party informed the political party registrar last Tuesday of the resignation and it automatically ended the term of the Pheu Thai executive board.
As the NCPO has prohibited political parties from conducting activities, Pheu Thai could not hold a meeting to elect a new executive board, he said. Pol Lt Gen Viroj Pao-in, the party's deputy leader, has been serving as acting leader.
Mr Charupong became the Pheu Thai leader in October 2012.
When the NCPO summoned Mr Charupong for talks in the week following the coup, Mr Charupong said he would defy the order and urged party members and supporters to join his anti-coup campaign. The military court issued a warrant for his arrest last Monday.
A Pheu Thai source said that Mr Charupong had left Thailand before the day of the coup.
However, some members of Pheu Thai have signalled an intention to cooperate with the junta. They discussed national reform with an NCPO working group at the Defence Ministry on Friday morning.
Those participating included Mr Chavalit, Pol Lt Gen Viroj, Pheu Thai legal expert Chusak Sirinil and Phumtham Vejjayachai,the party's acting secretary-general.
Mr Chavalit said the meeting was friendly and Pheu Thai was ready to cooperate with national reconciliation attempts. In the meeting Pheu Thai urged a democratic constitution and a national reform council that should include experts in various fields and permit public participation, he said.