Gilgit-Baltistan borders the Wakhan corridor of Afghanistan to the northwest, China's Uygur Autonomous Region of Xinjiang to the northeast, the Indian-controlled state of Jammu and Kashmir to the south and southeast, the Pakistani-controlled state of Azad Jammu and Kashmir to the south, and Pakistan's North-West Frontier Province to the west.

Until the war in North-West Pakistan, Gilgit-Baltistan was a major destination for foreign tourists, especially serious mountaineers, because it is home to five of the "eight-thousanders" and to more than fifty peaks above 7000 meters. Gilgit and Skardu are the two main hubs for expeditions to those mountains. The region is home to some of the world's highest mountain ranges—the main ranges are the Karakoram and the western Himalayas. The Pamir mountains are to the north, and the Hindu Kush lies to the west. Amongst the highest mountains are K2 (Mount Godwin-Austen) and Nanga Parbat, the latter being one of the most feared mountains in the world.

Three of the world's longest glaciers outside the polar regions are found in Gilgit-Baltistan — the Biafo Glacier, the Baltoro Glacier, and the Batura Glacier. There are, in addition, several high-altitude lakes in Gilgit Baltistan: