Officers searched the enormous building for several hours after the man handed a note to the finance department of the clinic claiming to have a hostage, reportedly a child.
The note demanded money and threatened that an explosive device would be detonated if cash was not handed over.
Special police commandos were called to search the clinic's 6,600 rooms but failed to find the man.
Initial fears that the clinic would have to be at least partially evacuated were not substantiated, although the complex was sealed off while the search was conducted.
"We haven't found anyone," a police spokeswoman said on Friday night.
The massive clinic building is one of the largest medical facilities in Europe. Besides caring for tens of thousands of patients each year, it houses the entire medicine department of the RWTH Aachen University.