Ganon's Tower was founded on June 26th, 1998 by Dan (aka Ganon). The site was originally known as "Zelda 64" and resided on FortuneCity. In September 1999, Dan took on the name "Ganon's Tower," and in February 2000 the site was picked up by ZeldaGames.com for hosting. Ganon's Tower acquired an eponymous domain name and relaunched with a new layout fourteen months later.
The first forum for Ganon's Tower was established in March 2001 at ezBoard and upgraded to an iKonboard the following fall. In 2002, Dan purchased a license for vBulletin, which operated until the site's closure.
After the closure of Hyrule.com.ar during the summer of 2002, Ganon's Tower became an impromptu refuge for forum members. The site would again become a refuge after Great Deku Tree closed at the end of 2004.
In 2008, Ganon's Tower changed management and the main portion of the site was removed, leaving just the forums. In June of 2010 the site announced it would be closing, and two months later, it was removed.
It was technically one of the oldest Zelda sites in operation, the oldest is North Castle.