Far-right historian Dominique Venner, 78, took out a gun while standing next to the main altar and shot himself through the mouth around 4 p.m. local time, police said, according to the BBC.
Police began the evacuation of the cathedral immediately, and it remained closed for four hours.
Witnesses said Venner made no statement before shooting himself but he did leave a note. Police declined to reveal its contents.
Monsignor Patrick Jacquin, the rector of Notre Dame, said he believed Venner's suicide was the first inside the cathedral in its 850-year history, although some had jumped from the building's twin towers.
"We will pray for this man as we pray for so many others who are at their wits' end," Jacquin said.
Venner had taken part in recent protests against the legalization of gay marriage, and posted a long essay on the subject on his website before killing himself. His historical work includes treatises on extreme nationalist themes, including supporting the ideology of the pro-Hitler Vichy regime during the Second World War.
He was also a member of the Secret Army Organisation, which opposed Algerian independence and tried on several occasions to assassinate President Charles de Gaulle.
Venner's suicide appeared to be his final act of protest against the gay marriage legalization. Not only did he choose a church altar -- the traditional spot for marriage ceremonies -- but his last posted writings pointed toward his belief for a need for drastic action.
"New spectacular and symbolic actions are needed to wake up the sleep walkers and shake the anaesthetised consciousness," he wrote.
"We are entering a time when acts must follow words."
Railing against the incursion of Sharia law and "Islamist control," Venner called for a protest to repeal the gay marriage law on May 26.
"It is here and now that our destiny is played until the last second," he wrote. "And these final seconds are as important as the rest of a lifetime."