Imam Mundhir Abdallah, who preaches in the Copenhagen neighbourhood of Nørrebro at the Masjid Al-Faruq mosque, which media have linked to radical Islam, is accused of citing a hadith or koranic narrative calling for Muslims to rise up against Jews.
"Judgement Day will not come until the Muslims fight the Jews and kill them," Abdallah said in a Facebook and YouTube video post in March.
"These are serious statements and I think it's right for the court to now have an opportunity to assess the case," public prosecutor Eva Rønne said in a statement.
This is the first time the prosecution has raised such charges under a criminal code introduced January 1st 2017 on religious preaching.
Rønne said it's legal to quote religious books like the Koran and the Bible, but that inciting or welcoming the killings of people could be punishable by up to three years in prison.
"It has always been illegal to accept killings of a certain group of people, but it's new for us to target hate preachers," she added.
Abdallah could face up to three years in prison if convicted under the hate speech law, Rønne told Ritzau.
The case will be brought before the Copenhagen district court but no trial date has been set, the prosecution said.
The Jewish community, which in May filed a complaint over the imam's speech, welcomed the prosecution's decision to press charges.
The community's head Dan Rosenberg Asmussen told TV2 that "there was no doubt about the intentions" of the imam's statement.
"It was deeply worrying," Rosenberg added.
Minister of immigration and integration, Inger Støjberg, who has been outspoken against Islamic practises in Denmark, has described the imam's address as "horrible, anti-democratic and abominable".
According to broadcaster DR, Omar al-Hussein, who was behind a series of shootings at a free-speech conference and a Jewish synagogue in Copenhagen in February 2015 which left two people dead, had visited the mosque the day before going on the rampage.
Denmark published in May 2017 a list of foreigners accused of preaching hatred -- five of them Muslim preachers and one Evangelical, banning them for at least two years.
The list included two Saudis, a Canadian, a Syrian, and two Americans, including pastor Terry Jones who burned copies of the Koran in 2011, and has since been updated on several occasions.