That self-imposed ban ended on March 3, allowing Thapa to resume his duties while Nepal took part in the first round of 2018 World Cup qualifying but his side lost 2-0 on aggregate to India after a goalless draw at home on Tuesday.
FIFA said the former AFC vice president had opted to stand down again, meaning he will miss the April 30 congress in Manama where his full-time replacement at regional level will be voted for.
"Ganesh Thapa... has agreed not to participate in any football-related activity at national and international level (administrative, sports or any other) for an additional period of 90 days as of 20 March 2015, while the FIFA Ethics Committee completes its review of claims involving alleged misconduct by ANFA officials," FIFA said.
FIFA had said in October the Nepalese FA had been the subject of an "unsatisfactory" external audit in 2012, when "unappropriated cash movements" were identified.
ANFA officials told Reuters last month that FIFA needed to complete a full investigation into how Thapa had run the body.
"The chaos in the administration of ANFA that has persisted for years under the leadership of Mr Thapa must be brought to an end. We urgently request your kind assistance," they wrote in a letter to the world governing body.
Thapa has long denied accusations of wrongdoing.
(Reporting by Patrick Johnston; Editing by John O'Brien)
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