Mr Mourinho could be seen entering the courthouse in the Madrid suburb of Pozuelo de Alarcon.
The court hearing comes two days before Manchester United is due to play Chelsea in the Premier League.
The manager held his pre-match press conference on Thursday, not Friday as is usually the case.
The Spanish authorities began a case against Mr Mourinho in June.
In 2015, Gestifute said, he accepted a settlement agreement regarding previous years.
"The Spanish government in turn, through the tax department, issued a certificate in which it attested that he had regularised his position and was in compliance with all his tax obligations," it added.
The allegations against Mr Mourinho come after investigations into several leading footballers in Spain.
Argentines Lionel Messi, Javier Mascherano and Angel Di Maria have all been punished for tax evasion while a case against Real Madrid star Cristiano Ronaldo continues. He denies wrongdoing.
More about: #Mourinho