The infirmary complex lies to the S of the cathedral, E of the E walk of the cloister, to which it was once connected by a vaulted passage known as the Dark Cloister. It consists of a nine-bay aisled hall running E–W, terminated by a stone screen at the E with a doorway or archway into the four-bay nave of the chapel. At the E end of this is a square-ended sanctuary vaulted in two bays. A doorway in the W bay of the chapel N nave aisle gave access to the monks' cemetery. Much of this survives, but it has been incorporated into later buildings. Except for the sanctuary of the chapel the roofs are gone, and the open passage remaining is now called Firmary Lane.

The N chapel arcade and the E bay of the N hall arcade were blocked for the construction of Alan of Walsingham's building, named after a sacrist and later prior of the monastery who was in office between 1321 and 1364, and probably begun in the 1320s or '30s. On the N side further W is Powcher's Hall, also begun in the 14thc. Thus the N chapel arcade and the first bay of the hall arcade are visible in the wall of Alan de Walsingham's Building. Pier 2 of the N hall arcade is lost, and bays 4 to 9 on this side are visible, built into the wall of Powcher's Hall. On the S, the chapel arcade is lost, and is now overbuilt by the Chapter Office. Further W, the wall of the Black Hostelry, a 13thc. building at least in part, incorporates bays 1–4 of the S arcade of the hall. The next two piers are missing, and bays 8–9 are visible in the wall of the Canonry House.

At the E the sanctuary of the chapel has been incorporated in the two-storey block containing the Chapter Office entrance and the Deanery. The Dean's Office, on the first floor, contains the upper part, including the vault. The alignment of the infirmary does not accord with that of the cathedral, but corresponds with a simple vaulted building to the S, and for Dixon (2003), 149 this indicates that it may preserve the arrangement of earlier buildings on the site. The arrangement of an aisled hall with a chapel at the E end is similar to infirmaries at Peterborough, Canterbury and (later) Chichester. The Infirmary complex was restored in 1989–96, and Horton-Krayenbuhl (1997) is an account of the survey carried out at that time.

No building dates are known, but the sculpture shows that the Infirmary workshop did not work at the cathedral, and indicates a date in the 1170s or '80s. The earliest dateable reference to an infirmary at Ely is in Liber Eliensis (386), when monks are said to have carried Archdeacon William to the infirmary where he died a few days later. His death is dateable between 1159 and 1169 (see Johnson (1984), 198), so it is just possible that the reference is to the present building, newly constructed.

The infirmary arcades in particular provide a spectacular display of the possibilities available to a sculptor working within the constraints of the scallop capital. Some similar, though less elaborate, forms may be seen in the Prior's House undercroft, and Pevsner has pointed out the connection with work at St Mary's, Ely, which is found in some of the simpler capital forms of the arcades and in the use of directional chevron.