Erdogan's nationally-televised remarks came after Turkish police detained four people over the weekend for depicting Islam's holiest site with pictures of the LGBT rainbow flag during a student protest.
"We will carry our young people to the future, not as the LGBT youth, but as the youth that existed in our nation's glorious past," Erdogan said during a televised video linkup with members of his ruling AK Party.
"You are not the LGBT youth, not the youth who commit acts of vandalism. On the contrary, you are the ones who repair broken hearts."
Rights groups accuse blame Erdogan of taking the mostly Muslim but officially secular country on an increasingly socially conservative course during his 18 years in power.
Turkey was hit by a wave of student protests last month that were sparked by Erdogan's appointment of a loyalist as the head of Istanbul's prestigious Bogazici University.
The protests have subsided thanks to a heavy Turkish police presence around the university's campus.
But one demonstration last week saw an artwork hung opposite the new rector's office depicting the holy site in Mecca and images of the LGBT movement's rainbow flag.
Turkish police accused four people of "inciting hatred in the population". Two of them have been remanded in custody and the other two placed under house arrest.
Turkish Interior Minister Suleyman Soylu branded the suspects "four LGBT freaks".
Erdogan had last month accused some of those taking part in the student protests of being "terrorists".
Homosexuality has been legal throughout modern Turkey's history.
But gay people often face harassment, and LGBT events -- including Istanbul Pride -- have been blocked under Erdogan.
