Prosecutors have charged Sukur with posting Tweets from his account @HakanSukur containing "insulting content against Mr President Recep Tayyip Erdogan and his son," the private Dogan news agency reported.
In his defence, Sukur, 44, said he did not intend to target the president in his posts, the content of which was not made clear.
But that was rejected by prosecutors, who claimed that the tweets were "clearly related" to Erdogan, the news agency said.
Sukur, a striker whose football career stretched from 1987-2007, was by far the most prolific goalscorer in the history of the Turkish national side, finding the net 51 times in 112 appearances.
He is also remembered for his electric performance in the 2002 World Cup, where Turkey registered its best ever performance of third place.
After football, the high-profile Sukur went into politics and was in 2011 elected MP from Erdogan's ruling Justice and Development Party (AKP).
Sukur had voiced objections to the government move to shut down the schools run by Gulen's movement Hizmet.
The legal case is one of a string of others targeting journalists, bloggers and ordinary people who land in court on charges of insulting Erdogan and other top officials.
Opponents say Erdogan has become an increasingly polarising figure in Turkey since becoming president in 2014 showing zero tolerance for any criticism on social media or on the streets.
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