The present building replaced a small wooden church, traces of which — including altar remains and old sill beams — were found beneath the chancel floor during a 1970s restoration. The stone church itself, comprising a rectangular nave with a later sacristy and porch, dates from around 1300, with walls up to 2.5 metres thick. A rounded medieval passage cuts through the nave's north-west corner, and a simple cross pattern of stones is set into the sacristy wall.
The original timber ceiling, thought to have been barrel-vaulted, was decorated with early Gothic ornamental paintings in white, grey-brown, grey and black, dated to around 1300; fragments of this early decoration have survived. By the later 15th century the timber roof was replaced with brick vaults — a star vault over the chancel and cross vaults elsewhere — and the walls and vaults were painted with figurative scenes, the chancel work attributed to a painter close to the workshop of Albertus Pictor. Further paintings in the westernmost vault probably followed in the early 16th century. These medieval paintings were later limewashed over in the 1850s, then uncovered and heavily restored in 1905, when missing sections were repainted and outlines reinforced — so much of what visitors see today reflects that early twentieth-century restoration as well as the original medieval work.
Among the furnishings, the granite font from Gotland dates to the 13th century, making it the oldest object in the church. The carved altarpiece, an early 16th-century Antwerp work depicting scenes from the life of Christ, is considered of notably high quality. Three medieval wooden sculptures — of Saint Gertrude, Saint Bridget of Sweden, and a Man of Sorrows figure — also survive. The pulpit, made around 1700 by Erik Hollner, is the second the church has had; its original blue-green colour scheme was overpainted within a few years, and the present colours are an attempted reconstruction of that early scheme.
Outside, a free-standing wooden bell tower north-west of the church is one of the oldest of its type in Uppland, with medieval structural features despite probably being built in the 16th century. Its base contains a stone-filled timber crib for stability, and its upper bell chamber is carried on sixteen heavy beams. Two bells hang within: a larger bell recast in 1786, and a smaller one dated 1641, said to have been commissioned in Scotland — reportedly ordered by a Scottish officer serving under Gustav II Adolf and his Swedish wife as a gift to their home parish, though how and when it came to Häverö is unclear.
The church's current organ was built in 1954 by H. Lindegren of Gothenburg, incorporating the case of an earlier 1863 instrument by Per Larsson Åkerman; it was subsequently modified in 1962.