The teens, a boy and a girl, were attacked by three schoolmates who followed them out of the school grounds in the Murcian town of Caravaca de la Cruz.
The three yelled "Poofter!" and "Dyke!" and "Perverts" as they followed the teens, Rubén López, a spokesperson with Spain's FELGTB gay rights group said, describing the attack.
The gay teens put up with the insults for a while "thinking they were going to stop", López said. Eventually though, the young boy turned to the aggressors and told them to leave him and his friend "in peace".
It was then that the three school students began to pelt the homosexual pair with stones.
"One of the stones hit the girl in the head. She lost consciousness and fell to the floor. They had to rush her to hospital," López said in a statement.
The attack only stopped when passers-by intervened.
The girl suffered bruising in the incident while the boy is "afraid, intimidated, humiliated and overwhelmed", the FELGTB spokesperson said.
The organization criticized Spain's education minister for the decision to scrap the socially liberal citizenship studies subject introduced by the country's former Socialist government in favour of the more conservative ethics course.
The head of the gay rights group No Te Prives, meanwhile, said Murcia needed to look at introducing tough new laws against homophobia like that passed recently in Catalonia.
That pioneering law — the first of its kind in Spain — will punish those who attack gays, lesbians, bisexuals and transsexuals with fines of up to €14,000 ($17,700).
Spain is one of the more progressive countries in the world on gay rights, with the country having legalized gay marriage in 2005 under the former Socialist government of José Luis Rodríguez Zapatero.