Madsen is set to help fill the gap after the sale of national team player Victor Froholdt, who moved to Portuguese FC Porto this summer.
In addition, Magnus Mattsson has since suffered a serious knee injury, and with the prospect of eight matches in the Champions League in addition to the Superliga and the Danish Cup competition, FC Copenhagen needed more manpower.
"This step feels absolutely right. FC Copenhagen is Scandinavia's largest club, and the ambitions of championships and European football appeal to me."
"I am looking forward to becoming part of the team and contributing with my strengths, and I am especially looking forward to playing in front of the fans both in Parken and away", says Madsen to fck.dk.
Sports director Sune Smith-Nielsen adds:
"It is no secret that we have been looking at Mads Emil for a long time, and with Magnus' injury, Mads Emil has become even more relevant to us."
"He can bring some of the qualities that we currently lack in our midfield constellation. That is why we are happy that we have now managed to reach an agreement with AGF."
As a replacement for Madsen, AGF have instead signed the Norwegain midfielder, Markus Solbakken, who arrives from Sparta Prague.