The 28-year-old, currently on loan at Elche from Sevilla, allegedly committed the offence on September 1, 2024, at his house in the town of Betera, in the province of Valencia.
Another player currently outside professional football, Pablo Jara, is also accused of sexual assault against a second victim "without carnal knowledge" at Mir's house on the same night.
The judge summoned both men to make statements on October 13, with Mir to appear via telecommunication.
"The investigating magistrate understands that the evidence gathered during the instruction of the case points to indications, not mere suspicions, that (Mir) sexually assaulted one of the two girls on two occasions," a judicial source told AFP.
Mir came through Valencia's youth academy and signed for Premier League team Wolves in 2018, before Sevilla bought him in 2021.
The striker was loaned back to Valencia in July 2024, after which the alleged sexual assault happened.
Mir was arrested in September 2024 and suspended by Valencia for two matches.