The city contains temples and step-pyramids, many with carved and decorated artefacts. Like many of the Maya cities of the area, it was abandoned at the end of the Maya Classic Era, for reasons that are not yet understood, about 1000 years ago.
The site was rediscovered by Teoberto Maler in 1905. He spent 3 months exploring, maping, and photographing the site. In the 1910s further investigations of the site were made by Sylvanus G. Morley and Oliver Ricketson.
Naranjo was one of the earliest site to suffer significant looting, as sculptures were removed for sale to collectors. Many of the ancient sculptures had already disappereared from the site in the 1920s. The problem got significantly worse in the 1960s, when many of the site's large sculpures were smashed into fragments by looters in order to remove and sell the fragments.
European and North American collectors have removed articles from the site, and since the Guatemalan civil war of the 1960s and 1970s, looting has become a major problem. It is claimed that the military governments of the time were complicit. Even now, archaeologists excavating the site are from time to time forced to abandon their work because of the lawless activities of the well armed looters.