Al Hussein - a FIFA vice president - is widely seen as a genuine reformer and his announcement is set to spark hopes that football governance could be overhauled.
The president of the Jordan Football Association believes it is time for football's headlines to be exclusively focused on what happens on the pitch by cleaning up FIFA's image off it.
FIFA are set to hold their next presidential election at the 65th FIFA Congress in Zurich at the end of May.
"I am seeking the presidency of FIFA because I believe it is time to shift the focus away from administrative controversy and back to sport," Al Hussein wrote on Twitter.
"This wasn't an easy decision. It came after careful consideration and many discussions with respected FIFA colleagues over the last few months.
"The world's game deserves a world-class governing body a service organisation and a model of ethics, transparency and good governance.
"The headlines should be about football, the beautiful sport, not about FIFA."
FIFA's reputation has been severely tarnished since they awarded the 2022 World Cup to Qatar and the subsequent revelations of bribery involved in that process.