Mayor Nutter had promised he would ask Pope Francis to "end judgment" of LGBT people by the church if he got the chance during the pope's visit.
On Saturday, the mayor raised the issue with the pontiff's audience as well.
Nutter, speaking at Independence Hall before the pope arrived to deliver an address on immigration and religious freedom, cited the mentorship of John C. Anderson, a gay one-term Philadelphia city councilman who helped launch Nutter's political career. AIDS took Anderson's life in 1983.
"In America, everyone has rights," Nutter said. "Our lesbian, gay, and bisexual citizens continue to fight for equality."
Nutter urged them to continue that effort.
"Keep fighting for your rights," he said. "It's a collective fight. And there are many others fighting with you."