The municipality is located on two islands in south Troms. Most of the municipality is located on Hinnøya, 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 Grytøya. Harstad is bordered by the municipality of Bjarkøy to the north, Kvæfjord to the west, and Tjeldsund (in the county of Nordland) to the south. To the southeast the Tjeldsund Bridge connects Hinnøya with Skånland and the mainland across Tjeldsundet, and to the northeast is the Vågsfjorden, where Harstad shares a water border with Ibestad. The city itself is located northeast on Hinnøya; it is the only city on the island, and is popularly known as Vågsfjordens perle (The pearl of Vågsfjorden).

Despite being located north of the Arctic Circle, Harstad incredibly features a subpolar oceanic climate with relatively mild winters and cool summers. Harstad does not have the brutal winters that most locations north of the Arctic Circle experiences. The city actually experiences warmer winters than major cities located 25 to 30 degrees farther south in latitude in the northern hemisphere such as Beijing, Chicago and Toronto. Summers in Harstad are cool, with average high temperatures seldom breaking the 22 °C (72 °F) mark. Mean annual temperature is 3.9 °C (39.0 °F) (1961–90) and annual average precipitation is 850 millimetres (33.5 in).[5] With high pressure weather, winter temperatures can get down to about −15 °C (5 °F), and in summer reach 27 °C (81 °F).