Gamla Uppsala was the original Uppsala: a royal seat, religious centre and meeting place for the Svear, reached by boat and sledge along the waterways of Lake Mälaren and the Fyris river. Tradition holds that a pagan temple once stood here, and some archaeologists point to postholes beneath the church, dated to the Iron Age, as possible evidence of an earlier cult site. This interpretation is contested by other scholars, and the question of whether a temple genuinely preceded the church remains a matter of ongoing academic debate rather than settled fact.
A stone cruciform cathedral in the Romanesque style was built on the site, becoming, in 1164, the cathedral of Sweden's first archbishopric. Around the mid-13th century fire severely damaged the building, prompting the construction of a new cathedral at Östra Aros, the settlement that would take on the name Uppsala. The fire-damaged cathedral at Gamla Uppsala was then downgraded to a parish church, and a further fire led to the demolition of its three-aisled nave and transepts in the 15th century, leaving the truncated central tower and apsidal chancel that visitors see today, now serving as nave and chancel.
The building's grey stone walls carry some decorative brickwork, including blind arcading on the gable above the apse and on the old central tower. Both the apse and the tower are thought to survive from the original, larger church, possibly begun around the mid-12th century. Some wooden furnishings, including one of three so-called triumphal crucifixes associated with the church, may also date from the 12th century. A runestone is set into the church's south wall.
The astronomer Anders Celsius is buried in the centre aisle of the church.
The present main organ was built in 1969 by Olof Hammarberg of Gothenburg, incorporating the case of an earlier 1806 instrument; a smaller mechanical choir organ was added in 1980.
The church lies on the Marialeden pilgrim route between Tegelsmora and Gamla Uppsala, which continues via the Eriksleden to Uppsala Cathedral; pilgrim passes and stamps are associated with churches along these paths.