The High Septon during the time of King Aegon I Targaryen built a large sept upon the hill after moving to the city from Oldtown, where he had previously had his seat be at the Starry Sept. During the Faith Militant Uprising, King Maegor I Targaryen lifted the flag of House Targaryen upon Visenya's Hill to rally his supporters.
The pretender boy King Gaemon Palehair, who claimed to be the bastard son of King Aegon II Targaryen, called thousands of followers to the hill where he issues his edicts. Soon after, however, his mother admitted he wasn't the child of the king and she was executed, although Gaemon himself was spared.
Construction of the current Great Sept began under the rule of the pious king, Baelor I Targaryen. The sept was, thereafter, named after the king.
A Feast for CrowsEdit
The wake of Lord Tywin Lannister was held at the Great Sept of Baelor.