McAllister received an offer for another job and his last day is Feb. 11, according to Chairman Jack Sapia.
He would not disclose the new job and McAllister, who recently became the target of a proposal to eliminate his position, could not be reached for comment late yesterday.
"He had a small window of opportunity and had to do what was in the best interest of his family," Sapia said. "We'll miss Russ."
The town administrator resigned during the nonpublic session Monday night and told Town Hall employees yesterday that he had given his notice.
McAllister first came to Atkinson as interim town administrator in July 2004 and was hired later that year to permanently replace Town Administrator Victor "Vic" Richards, who died after suffering a heart attack.
McAllister previously worked as the city manager of Rochester for two years. He earned $62,005 in 2006, the latest year for which salary figures are available.
The town administrator's position is the target of a local taxpayers group that submitted a warrant article by citizens petition to eliminate the post and revert to a selectmen's clerk.
The petition was submitted a few weeks ago by Leon Artus, head of Atkinson Taxpayers for Fair Evaluations Committee, and was intended specifically for McAllister.
Artus filed a written complaint with the selectmen earlier this month because he said the town administrator did not fulfill a Right-to-Know Law request.
"It's a double-edged sword. When you go after someone, who says they'll stay?" McAllister said at the time.
But Sapia said last night that McAllister has a lot of "backbone" and wouldn't let a small group of angry residents chase him out of Atkinson.
"I think people will miss, well a majority of people will miss, what he brought to the town," Sapia said.
Sometimes when a person comes up with ideas that are different from how things have always been run, people get upset, Sapia said. But he said McAllister has a "wide diversity of assets" from which Atkinson benefited.
Selectmen have yet to formally discuss how they will replace McAllister.