Housed in what was once the presidential palace — the former seat of Honduran government before the capital moved to Tegucigalpa — the Archaeological Museum focuses on the Lenca civilisation and the El Cajón archaeological project. The Lenca were the dominant Indigenous culture of western Honduras and El Salvador before the Spanish conquest, and Comayagua was close to the center of their territory.
The collection includes ceramics, stone carvings, and everyday objects from Lenca sites in the region, plus exhibits on the colonial period. The building itself is worth seeing: the former palace is one of the few surviving examples of colonial civic architecture in Honduras. Small admission fee; open Tuesday through Sunday.