The 26-year-old suspect is believed to have groped a woman while he and around 10 other men surrounded her at the city's main train station, a spokesman for the Cologne administrative court told AFP.
"The first sexual assault charge has now been filed," the spokesman said, nearly three months after the events that inflamed public debate about a huge influx of refugees and migrants to Germany.
The Algerian national, who was not named, is also accused of stealing the victim's mobile phone from her handbag.
It was not immediately clear when the cases would go to trial, the spokesman added.
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Prosecutors received more than 1,100 criminal complaints over incidents on New Year's Eve in Germany's fourth biggest city, including over 480 accusations of sexual assault, news agency DPA reported.
Most of the 120 suspects are from Algeria or Morocco, including recent arrivals and men who have been in Germany for years.
Only three people have been convicted in the ensuing months, for theft, and the city's police chief conceded in February that most perpetrators may never be caught.
Far-right groups railed against "sex jihadists" and "rapefugees" in street rallies and the events were seen as pivotal in delivering strong results to a populist anti-migrant party, the AfD, in three state elections this month.