The suspension centres on an internal feud at the PFF. This led a court to appoint an administrator to run its affairs in violation of FIFA requirements that such a body be managed independently.
"The PFF representative and club teams are no longer entitled to take part in international competitions until the suspension is lifted," FIFA said in a statement.
Senior PFF official Colonel Ahmed Yar Lodhi said he had long anticipated the ban following the government's intervention in the federation's affairs.
"We are FIFA's recognised body but the government interfered in our affairs and did not let us work," Lodhi told AFP.
"This situation was unacceptable for FIFA and they have now decided to impose a ban on Pakistan membership, which is very unfortunate."
In 2015 FIFA suspended Indonesia over government meddling in the country's football association. It lifted the suspension the following year.
The ban on Pakistan comes as neighbour and arch-rival India hosts the U17 World Cup.
Pakistan boasted a top place in Asian football until the early 1970s, but a lack of government support and poor infrastructure helped push them as low as 200th currently in the FIFA football rankings.
The game is growing in popularity once more, however, even in a country obsessed with cricket.