The incident, at the medal ceremony following the Spanish women's team's World Cup victory in Sydney, Australia, last month, unleashed a wave of indignation against sexism and macho behaviour in Spain.
Rubiales had refused demands from many players, sports bodies and politicians to quit his position as president of the Royal Spanish Football, saying he had done nothing wrong and the kiss was mutual and consensual.
However, the furore did not die down and on Sunday he resigned after Hermoso lodged a criminal complaint against him.
He will appear before the court at noon on Friday.
The complaint by Hermoso describes how Rubiales kissed her on the mouth "without her consent" while holding her head with both hands after Spain defeated England in the women's World Cup final on August 20th.
The incident took place in front of a global television audience.
High Court judge Francisco de Jorge is in charge of the probe as the incident took place outside Spain.
Rubiales has not responded to Reuters' questions about the case.
