The unsolicited kiss, broadcast live on August 20 after Spain’s victory over England at the Women’s World Cup final in Australia, has triggered protests over sexism in Spanish sport and wider society.
Ms Hermoso laid a complaint of sexual assault and Judge Francisco de Jorge issued an order for Mr Rubiales to answer his questions at Spain’s National Court in Madrid.
Mr Rubiales did not speak before entering the courthouse with his lawyer.
He kissed the Spanish forward on the lips during the awards ceremony in Sydney. He said Ms Hermoso had consented to the kiss, but she has denied that repeatedly.
Spanish state prosecutors formally accused Mr Rubiales last week of alleged sexual assault and an act of coercion when, according to Ms Hermoso, he pressured her to speak out in his defence immediately after the scandal erupted.
Mr Rubiales announced on Sunday that he was resigning from his post, from which he had already been provisionally suspended by FIFA.
Judge de Jorge is carrying out the preliminary investigation into the accusations against Mr Rubiales, and will then decide whether the case should go to trial.
According to a sexual consent law passed in Spain last year, Mr Rubiales could face a fine or a prison sentence of one to four years if found guilty of sexual assault.
The new law eliminated the difference between “sexual harassment” and “sexual assault,” sanctioning any non-consentual sexual act.
Following his resignation as Spanish FA president, Mr Rubiales said in a statement: “After the rapid suspension carried out by FIFA, plus the rest of proceedings open against me, it is evident that I will not be able to return to my position.
“Insisting on waiting and holding on is not going to contribute to anything positive, neither to the federation nor to Spanish football.”
The former footballer initially refused to back down in the face of criticism from politicians including Spain’s Prime Minister, its men’s and women’s football teams and international stars including the Lionesses.
Meanwhile players in the Spanish national women’s team are set to continue their boycott of the squad, Cadena SER radio station reported on Friday, citing unidentified sources close to the federation.
The team informed the Royal Spanish Football Federation (RFEF) that they maintain their resignation from the national team after the Rubiales case, the radio station reported.
On August 25, Ms Hermoso and 80 other players and former players signed a joint statement in which they demanded “real changes, both sporting and structural”.