"The headlines should be about football, not about FIFA," he added, without mentioning Blatter.
Fifa has been dogged by a number of corruption allegations. There was an investigation last year into bribery allegations relating to the World Cup bidding process. Russia won the bid to host the 2018 tournament and Qatar, a nation with little soccer history, is set to host the 2022 World Cup.
Fifa's governing body was marred by further controversy last month when the lawyer investigating the charges resigned two years after he was appointed by Blatter. Former U.S. attorney Michael Garcia clashed with Fifa after it failed to publish his full report into the corruption and bribery allegations.
Prince Ali's reputation is untainted when it comes to Fifa, however. He has been credited with pushing the organization to lift the ban on hijabs – headscarves worn by some Muslim women – in women's soccer.
Read MoreQatar soccer World Cup moved to winter: FIFA Official
"The message I heard, over and over, was that it is time for a change. The world's game deserves a world-class governing body — an International Federation that is a service organisation and a model of ethics, transparency and good governance," Prince Ali said.
Fifa declined to comment on the Prince's decision to stand for president.
The election takes placed on May 29 in a secret ballot and candidates wishing to run need to apply before a January-29 deadline. A candidate needs two thirds of the vote to win.
Former diplomat Jérôme Champagne is the only other person to join the presidential race to date.