Danish lawmakers meanwhile passed new legislation making it treason to join "hostile armed forces" like IS.
"It is the prosecution's view that everyone who joins IS in Syria has agreed in principle to take part in the terrorist acts that IS commits in the country," prosecutor Lise-Lotte Nilas said in a statement.
The 23-year-old man faced charges over "agreeing to be recruited to commit terrorist acts" and for "violating the ban against supporting terrorism," she said.
The latter charge was over carrying 20,000 kroner ($2,935, 2,680 euros) with him when he was arrested by Danish police in March this year as he attempted to return to Syria.
If found guilty he would face over four years in prison.
The prosecution said it would also seek to strip the man of his Danish citizenship if Turkish authorities confirm he is a dual Danish-Turkish national.
At least 125 people have left Denmark for Syria and Iraq since the summer of 2012, according to the Danish Security and Intelligence Service, but until now authorities have been unable to prove that any of them had joined IS.
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The trial is expected to open in the spring, the prosecution said.
In neighbouring Sweden, a court on Monday sentenced two men to life in prison on terrorism charges over their role in two "cruel and brutal" murders in Syria in 2013.
Also on Tuesday, the Danish parliament passed legislation making it treason to join "hostile armed forces" like IS, a crime punishable with a sentence of life in prison.
Under the new rules, recruiting people into such groups can lead to 16 years in jail.
"There must be serious consequences for people living in this country if they turn their back on Denmark and go to fight under the extremists' flag or encourage others to do so," Justice Minister Soren Pind said in a statement.
Separately, Danish police lowered the country's threat level on Tuesday, a month after raising it to the second-highest on a scale of five in the wake of the November 13 attacks in Paris.
"After an overall assessment, including discussions with the Security and Intelligence Service (PET), we believe that the police can handle the current situation with 'heightened preparedness'," police inspector Jorn Aabye said in a statement.
Denmark's threat level was raised to "significantly heightened preparedness" -- one notch below the highest level -- for the first time ever on November 17. Police cited the "uncertain situation in a number of European countries."
Intelligence agency PET said its "serious" threat level was unchanged.