"The pilot of the airplane has died as a consequence of the accident, which happened during take-off," the Spanish defence ministry said in a tweet following the crash near the Torrejon de Ardoz base, around 20 kilometres (12 miles) from Madrid.
The crash was due to a loss of power, the defence ministry said.
Interior Minister Juan Ignacio Zoido named the pilot as 26-year-old Fernando Pérez Serrano.
Descanse en paz Fernando Pérez Serrano, un joven piloto de 26 años que ha fallecido en acto de servicio. Todo el cariño a su familia. https://t.co/Gflp9r7Q70— Juan Ignacio Zoido (@zoidoJI) October 17, 2017
The accident came just days after the pilot of a Eurofighter jet was killed Thursday on the approach to landing at a military base at Albacete, 300 kilometres southeast of the capital.
The jet had been taking part in a military display for Spain's national day.
Two other Eurofighter jets crashed in Spain in 2010 and 2014, both times killing the pilot.