Fátima is Portugal's most important Catholic shrine, drawing hundreds of thousands of pilgrims each year.
The man found dead was a native of Rio Maior who was 68, according to the Santarém region GNR.
Basilica officials "heard a shot and when they arrived found the gentleman dead," the GNR official said.
According to a church official, "between 9.15 and 9.30 security came across a man alone inside the basilica who unfortunately was already dead". The shrine "deeply regrets the death of a person", the official added.
In an earlier statement, the shrine said that it was "temporarily closed to the public" because of "a suicide attempt that unfortunately ended with the death of a man".
No one else was in the basilica at the time except for shrine security "who immediately ran to help this brother" and called the emergency services.