The decision comes after a meeting between FIFA president Sepp Blatter and Gambia sports minister Alieu Jammeh in Zurich on Tuesday, in which it was agreed a "normalisation" committee would take over the running of the FA's affairs with elections due to be held by the end of September.
The deal sees off the threat that the Gambia could be excluded from June's start of the group stage of Africa's qualifiers for the 2014 World Cup in Brazil.
"The tasks assigned to the normalisation committee include the adoption of new statutes in line with FIFA recommendations and the organisation of the elections of a new board according to the new statutes," a FIFA spokesman said in a statement to Reuters.
Gambia's government dissolved the country's FA earlier this month in reaction to a 2-1 home defeat by Algeria at the start of the 2013 African Nations Cup qualifiers.
The country was initially threatened with expulsion from world football by FIFA, which usually takes a strong stance against state interference in the affairs of member associations.
However, Tuesday's decision effectively endorsed the removal of the current leadership of the Gambia FA.