In the painting, Christ, naked but for a loincloth, is bound to a marble column that rises up the centre of the scene, dividing it into two halves.

Tall city buildings in the background are depicted with Byzantine reverse perspective frame the scene.

The figure of Christ is heavily influenced by that in Cimabue's Santa Croce Crucifix, while the torturers in bright clothing recall the Sienese School and the stylised background buildings the Roman school, the latter influence already taken on by Cimabue's workshop in the Lives of the Apostles in the Upper Basilica at Assisi.

The physical condition of the paint at the edges of the Flagellation of Christ panel indicate that it was at the lower-right corner of a larger composite work.

Two other scenes by Cimabue, painted on wood panels of similar size, have been identified as parts of the same altarpiece: the Virgin and Child with Two Angels in the National Gallery in London (discovered in 2000) and The Mocking of Christ in the Louvre (discovered in 2019).