Elton are leaving the Bolton Association at the end of the season to join the Central Lancashire League.
The club tended their resignation at a meeting of the Association hierarchy last night when it was accepted.
Association chairman Frank Jackson said: "Elton have wanted to go a couple of times in the past so I think it is third time lucky for them.
"They tended their resignation letter and it was accepted.
"Everything was done how it should be done by them and by the Central Lancashire League.
"They thanked the league for everything we have done for them and we wished them well for the future."
On rumours that other clubs are looking to join other leagues, he said: "We are happy that all the other teams seem to be happy with what we are doing in the Bolton Association.
"There has been a rumour mill that has just started up that clubs are looking to leave but that doesn't look to be the case.
"Because of the rumours some of the new clubs who have just joined us were starting to wonder if they had jumped out of the fire and into the frying pan.
"I can understand that but I think they are seeing that the Bolton Association is run differently to the Manchester Association."