Francesco Borromini built a cloister at San Carlino in the large space between the convent building and the public road. For its construction he was inspired by the typical atriums of ancient Roman houses, with a well in the middle of the cloister to collect rainwater.

The cloister is rectangular in plan - although its angles were replaced by convex curves - and has a double level of elevation.

The first level consists of pairs of Tuscan columns supporting a Palladian window that runs around and encloses the entire perimeter of the cloister. The inner gallery of the first level is covered by a continuous barrel vault, which subtly crosses, without edges, the other shorter vaults that start perpendicularly from the arches of the Palladian windows.

The upper level is also made up of pairs of Tuscan columns, in line with those of the lower level, but smaller in section and height, thus giving the cloister an optical sensation of greater elevation. The columns on this second level are crowned with octagonal capitals, which support a lintelled structure that runs along the entire perimeter of the cloister in a straight line. In the balustrade of this second level, which is clearly Baroque, the alternating straight and inverted balustrades of the parapet are striking.