After leaving the brief closed-door hearing, the 54-year-old told reporters he had paid everything he owed to the Spanish tax office.
Prosecutors allege Mourinho owes the Spanish state nearly £2.9million in undeclared revenue relating to image rights in 2011 and 2012.
"Two years later I was told that an investigation had been opened and that to regularise my situation I had to pay a certain amount".
Speaking to reporters outside Pozuelo de Alarcon Court of Investigation number four before jumping in a taxi to leave the area, he added: "I answered, I didn't contest it, I paid and I signed an official agreement with the state under which everything was definitively closed".
"I left Spain in 2013 with the information and the conviction that my tax situation was perfectly legal", Mourinho said. "That is why I am here, nothing else".
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Mourinho did not say how much he had to pay.
The Portuguese denied the charges, saying he had paid €26m in taxes during the three years he lived in Spain as Madrid coach and had previously "entered into a settlement agreement regarding 2013".
The court date could not have come at a worse time for the Portuguese, with his United side facing Chelsea on Sunday. Accused of a €14.7m fraud, Ronaldo did not accept the investigator's understanding of his affairs and during a 90-minute hearing in July he told the judge he had done nothing wrong and was only being targeted due to his fame.
With a host of allegations of tax fraud hounding the footballing world as of late, the most notable cases being that of Neymar Jr and Lionel Messi, Mourinho will be glad to relieve himself of the burden that such charges carry.
The money involves revenues from image rights, not salary paid by Real Madrid. Di Maria and Carvalho are reported to have settled their cases, while those of Falcao and Coentrao are still being contested.