The building they pulled down had been unlucky for six hundred years. Begun around 1130 in granite and sandstone, with a long nave, stubby transepts and two slim-spired towers over the west front, it burned in 1501, burned again in 1567, and then on 27 June 1726 it burned catastrophically along with most of eastern Viborg, leaving nothing but bare walls and vaulting. What went up afterwards was a Baroque shell wrapped around medieval remnants, so poorly built that it was failing by 1770. The towers were capped with squat domes that locals, who remembered the old spires, called coffee pots. Between 1800 and 1814 the church was closed for want of money and used to store grain.

N. S. Nebelong and Julius Tholle drew up the rebuilding, and Tholle wanted to salvage as much medieval fabric as he could. He died in 1871, before the work was done, and H. B. Storck took over; the older sections judged unsalvageable came down. The new cathedral was built in brick and then faced in granite, which bought the look of a granite church at a fraction of a granite church's price. Its model was Lund Cathedral in southern Sweden. When it was consecrated in 1876 the result was controversial, and it still deserves the argument: what stands in Viborg is a nineteenth-century reconstruction of what nineteenth-century architects believed a Romanesque cathedral ought to look like.

The oldest surviving part of the church is underneath it. The medieval crypt beneath the choir has three aisles carried on six granite columns, and parts of the foundations of an earlier stone cathedral can still be read in the masonry. Above it lies the grave of King Erik Klipping, murdered in a barn at Finderup outside Viborg on the night of 22 November 1286 — tradition counts fifty-six wounds — and buried before the altar here. Fire destroyed the grave along with everything else, and what little remained of him was reinterred beneath the choir floor. For a century after the Reformation, Viborg went on saying prayers for Erik Klipping's soul, long after every other Danish church had stopped, until 1630.

An empty new cathedral needed something on its walls, and the medieval frescoes had gone up in smoke in 1726. Between 1901 and 1906 the painter Joakim Skovgaard filled the interior with biblical scenes — vaults, arcades, the great expanses of plaster over the nave — in deliberate echo of the kalkmalerier the fire had taken. He added ceiling paintings in oils in 1913. It is his masterwork, and it is the reason most visitors come: not the granite, which is a copy, but the painting, which is not. The Skovgaard Museum, founded in 1937, stands next door and is devoted to the artist's family.

Because 1726 consumed the entire contents of the old church, nearly everything inside today either arrived from somewhere else or was made after 1876. A carved tympanum from the medieval building was set over the south door, and two old carved stones were given one more life in the apse. The seven-branched candelabrum on the altar was cast in Lübeck in 1494. The altar itself is a copy of the gilded medieval "Golden Altar" at Sahl Church, made in that style by C. C. Peters, and the sandstone pulpit was carved for the new building by Rosenfalk after the manner of H. W. Bissen. Even the bells are replacements: the medieval ring perished in 1726, and of the five now hanging in the towers the oldest was cast in 1730 by Caspar Kønig, with later additions in 1837 and 1896.