Zanzibar, which is officially part of Tanzania but has its own government, was given unanimous approval at the Confederation of African Football's general assembly in March.
The archipelago has long hoped to become a member of the international football community and had its previous application rejected by Fifa in 2005.
"Following admission of Zanzibar into CAF, TFF has now formally submitted application for Zanzibar to become a member of FIFA.," TFF president Malinzi wrote on his official Twitter account on Sunday.
The Zanzibar Football Association (ZFA) has already fulfilled a crucial requirement which states that national associations must be affiliated to continental confederations before they can join Fifa.
Should Fifa accept Caf's 55th member association, then it will become the 212th member association of world football's governing body.
It will also be granted the right to vote on global football issues and the national team will be able to take part in the 2022 World Cup qualifying competition.
Zanzibar was previously an associate member on the continent, allowing its clubs to play in Caf competitions but its national team was excluded.
The semi-autonomous territory is expected to participate in the 2021 Africa Cup of Nations qualifying.
Tanzania's Football Federation (TFF) president, Jamal Malinzi, has confirmed Zanzibar's fresh bid to become a member of Fifa.