Quelccaya lies in the tropical highlands of southern Peru, within the eastern Andes in the Cordillera Oriental. ten kilometres (6.2 mi) northwest of Quelccaya lies the Cordillera Vilcanota mountain range, which it is sometimes considered to be part of; occasionally Quelccaya is also linked to the Cordillera Carabaya range. East of Quelccaya, the Andes drop off steeply to the Amazon basin and the Amazon rainforest is only 40 kilometres (25 mi) away; supposedly it can almost be seen from the summit of Quelccaya. 120 kilometres (75 mi) south of Quelccaya lies Lake Titicaca. Politically, Quelccaya is part of the Cuzco Department.
The Andes in Peru, Ecuador and Bolivia are subdivided into several separate mountain ranges, many of which are glaciated above 5,000 metres (16,000 ft) elevation. Peru contains about 70% of all tropical glaciers, and Quelccaya together with ice bodies in New Guinea and the Rwenzori Mountains in Africa is one of the few tropical ice caps in the world, or even the only one; during glacial times there were more ice caps which may have resembled Quelccaya. In 1968, the existence of two smaller ice caps south of Quelccaya was reported.
The ice cap, which is also known as Quenamari and is sometimes also spelled Quelcaya, lies in a remote area. A road gets within 40 kilometres (25 mi) from the ice cap, which can be reached within three days with pack animals. There are several camps at Quelccaya, including one close to the northwestern ice margin. A 1974 map shows a homestead on the Huancané River southwest from Quelccaya, about 12 kilometres (7.5 mi) from the ice margin. Quelccaya is part of the
Quelccaya National Sanctuary, a protected area, and the local population considers Quelccaya an important apu, a holy spirit. The cities of Cuzco and Sicuani lie 130 kilometres (81 mi) northwest and 60 kilometres (37 mi) southwest of Quelccaya, respectively, but the region around the ice cap is only thinly populated.