The game's governing body withdrew the suspension it imposed on the NFF, which meant no Nigerian team, including club sides, could play internationally, on Friday after its president, executive committee and congress were reinstated.
A FIFA statement said: "FIFA has noted that the court proceedings and order preventing the president of the NFF, the NFF Executive Committee members and the NFF Congress from running the affairs of Nigerian football that prompted the suspension have been withdrawn.
"As statutory order has been reinstated at the NFF and the legitimate bodies reinstalled, FIFA has decided to lift the suspension as of today, Friday 18 July 2014.
"The lifting of the suspension means that all rights of the NFF as a FIFA member as defined in article 12 of the FIFA Statutes are reinstated."
FIFA acted on July 9 after the executive committee was sacked in the wake of Nigeria's exit from the World Cup finals in Brazil.
The move came after FIFA's warnings to return power to the executive committee went unheeded with an extraordinary general assembly of the federation taking place in Abuja without NFF chief Aminu Maigari, his executive committee and the NFF congress having been restored to power.
Maigari had been arrested on his return from South America, where Nigeria reached the second round, only to bow out after a 2-0 defeat by France in the last 16, but was later released.