The club announced it on its website on Monday, reports Xinhua.
The 64-year-old Bayern official, who had been in office from 2009 to 2014, stepped down after he was convicted of tax evasion for 28.5 million euros ($ 31.5 million).
In February, Hoeness was released from jail after having served half of his three-and-a-half-year sentence with the rest of his jail term suspended for good conduct.
After Hoeness' release, German media had already speculated about his comeback to Bayern presidency. However, Hoeness said in March that he needed time to clear his head before making a statement on his future.
The scheduled election of the president's chair will be held at Bayern Munich's upcoming annual general assembly in November. All present club members are eligible to vote.
Current Bayern president Karl Hopfner will no longer run for office, as Hopfner and Hoeness have mutually agreed on this.
Hoeness, who scored 86 goals in 239 matches from 1970 to 1979, lifted the European Championship in 1972 and the World Cup in 1974 for Germany.
After his professional career, Hoeness became Bayern's sporting director for 30 years before he was appointed the club president in 2009.
On August 26, Bayern Munich will kick off its new Bundesliga 2016-17 campaign against Werder Bremen.
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