A police spokesman said a special unit was defusing explosives which they had found on the man's body at the school in Emsdetten near the Dutch border.
The police would not say how the man had died.
A teacher said he was an 18-year-old former pupil of the school, but police refused to confirm this.
The man had fired several shots after entering the school at around 9:30 am (0830 GMT), according to a police spokesman in the nearby city of Muenster.
A teacher and a caretaker suffered minor injuries after they tried to confront the intruder.
The school was evacuated and all the students, aged between 11-16, were taken to safety, the police spokesman said.
"All the children are safe," the spokesman told AFP.
The television news channel n-tv reported that the injured teacher was pregnant.
The police had tried to negotiate with the man before he died.
Police said they could not confirm reports that he had tried to take hostages.

Copyright AFP (Agence France-Presse), 2006