The bomb was found Wednesday during routine checks at a building site at Damaschkeplatz Square, near the city's train station, The Local.de reported.
City authorities ordered the evacuation of nearby residents as a precaution. A nursing home and hospital were among buildings evacuated.
A controlled explosion of the bomb was scheduled for Thursday evening, officials said.
A large portion of Magdeburg was destroyed during World War II and several unexploded bombs have been discovered in the city.