The accident came barely two weeks after two people died at the World Cup stadium in Sao Paulo which is scheduled to host the event's opening match in June.
It was also the second fatal accident to hit the Manaus venue. Manaus is the capital of the Amazonia region, far north of Sao Paulo and Brasilia.
Brazilian media said the dead man was a 22-year-old construction worker who died in the early hours of Saturday after falling 35 meters (115 feet) from the stadium's roof. The venue will host England's opening match on June 15 against Italy.
Saturday's tragedy is the fourth to hit preparations for Brazil's first World Cup since 1950. The country is racing to be ready for the event.
One fatality was recorded at a new stadium in Brasilia while in Sao Paulo two people died on November 27 after a crane dropped a piece of roofing on them.
The Sao Paulo arena will not now be ready until mid-April -- less than two months before the June 12 kick-off between Brazil and Croatia.
Construction firm Andrade Gutierrez said an investigation of Saturday's incident would immediately be opened.
Only last Tuesday, Manaus coordinator Miguel Capobiango Neto had assured reporters the venue would be ready for December 20 in time for an inauguration on January 15.