The municipality is located on two islands in south Troms. Most of the municipality is located on Hinn�ya, which is Norway's largest coastal island (three islands in the Svalbard archipelago are larger). The northern part of the municipality is located on the southern half, 53 square kilometres (20 sq mi), of the island of Gryt�ya. The Andfjorden lies west of Gryt�ya. Harstad is bordered by the municipality of Bjark�y to the north, Kv�fjord to the west, and Tjeldsund (in Nordland county) to the south. To the southeast, the Tjeldsund Bridge connects Hinn�ya with Sk�nland municipality and the mainland across Tjeldsundet, and to the northeast is theV�gsfjorden, where Harstad shares a water border with Ibestad municipality. The city itself is located on the northeastern part of on Hinn�ya; it is the only city on the island, and is popularly known as V�gsfjordens perle (The pearl of V�gsfjorden).
The municipality contains several small islands, including Arn�ya, Gressholman, Kje�ya, Kj�tta, Kj�ttakalven, M�ga, Rogla, Lille Rogla and �ker�ya.
The highest mountain in Harstad is S�tertinden, which is 1,095 m (3,593 ft) above sea level. It is located near the village ofSandtorg in southern Harstad. The 412-metre (1,352 ft) tall mountain, Nupen, is located in the northwestern part of the municipality on the border with Kv�fjord
