The ban has been in place by Fifa for the past three years and has involved exclusion from press conferences, threatening letters, and a persistent refusal to answer questions regarding serious charges of maladministration.
The IFJ argue that to persist with the ban would undermine the bodies’ commitment to transparency.
"The Jennings experience illustrates just how difficult life becomes for investigative journalists when powerful institutions give the impression they are answerable to no one and beyond criticism," said Aidan White, IFJ General Secretary.
The IFJ says Fifa should follow its declared principles of openness and co-operate fully with Jennings and other investigative reporters.
"Public trust depends absolutely upon open and accountable government and Fifa should be in the forefront of setting standards of transparency," said White in a letter to Fifa President Sepp Blatter.
The ban on Jennings, who is renowned globally for his journalism and exposing of corruption, was imposed after newspaper and television reports alleged bribery, secrecy, and corruption within the organization.
Blatter himself has been accused of unusual secrecy regarding his salary, bonuses, perks and allowances from Fifa.
The IFJ argue the ban is systematic of the problem of institutional hostility towards investigative journalists.
"His trenchant and independent reporting has delivered some hard truths that, although unpalatable to some, contribute to an important public debate about the need for reform and change," said White.
"The world of sports needs to become more aware of its public responsibilities and needs to outlaw internal secrecy. Fifa can lead the way by ending this ban and by answering legitimate questions, no matter how difficult they may be, honestly and in full."