A portal on the south wall of the anti-sacristy provides access to the upper cloister. From its beginnings, the "claustra nueva" (new cloister) of this cathedral has had a double floor plan to accommodate the steep slope between the floor of the church and the Calle de la Paloma. Its construction dates back to the end of the 13th century and features an irregular rectangular floor plan with six arches on the east and west sides and seven arches on the north and south sides. The cloister of Pamplona Cathedral, also known as the upper cloister or high cloister, was designed by the master Enrique and is considered "an outstanding example of Gothic art" by Vicente Lampérez. The cloister's galleries are covered with four-partite, simple ribbed vaults, and the cathedral's large windows feature pointed arches, triple mullioned windows, and tracery of three quadrilobed oculi.

The cloister's outward look.
The blind arches of the north gallery feature statues depicting characters or scenes from the Old Testament, like the Sacrifice of Isaac; the vegetal ornamentation of its arcades, capitals, and archivolts of its walls are precious; and most importantly, the historical decoration of its four corner pillars features sculptural groups representing the Annunciation, the Epiphany, and groups of figures related to the construction of the cathedral. Numerous canons of the cathedral are buried beneath the blind pointed arches of the side walls of the other three galleries, which date from the 12th to the 16th century. Romanesque tomb of Doa Godo, mother of Alfonso VIII's steward, who died in 1105; Gothic tomb of Bishop Mateo Rynal, who died in 1259; Renaissance tombs of Canons Juan López del Hospital and Diego de Santander, both from the 16th century and carved by Diego de Siloé; and the Renaissance tomb of Canon Gaspar de Illescas, from the 17th century. The tomb itself, with a recumbent statue on the lid and coats of arms on the front, decorated with grotesques and fleurons, can be found in the lower section, while the upper section features two medallions with the effigies of St. Peter and St. Paul, a relief with the scene of the Birth of Christ, and four niches with statues of the Fathers of the Western Church.

The Gothic chapel of San Jerónimo, or of Mena, with a square floor plan covered with a starred rib vault, was built by Juan de Vallejo in 1545 at the request of Canon Francisco de Mena, who died in 1553 and whose Renaissance tomb, with a recumbent statue and a beautiful polychrome relief representing the Coming of the Holy Spirit, is attached to the northwest corner of the galleries.

Cloister, Lower
Although its floors have been lowered, the lower cloister, which served as a cemetery for centuries, was constructed about ten years before the upper cloister and is noticeably less slender; it was restored, according to many, almost reinvented, by Vicente Lampérez, between 1899 and 1911, who, following the "purist" criteria of Viollet-le-Duc, lowered the floors, replaced the tracery in its arcades, except in those of the south gallery that These galleries and the chapel-crypt of San Pedro, which is thought to have belonged to the Romanesque cathedral and which can be accessed from the north gallery, now house an interpretation center on the cathedral's construction and, in addition to models of the Romanesque cathedral and information panels on its history, house archaeological and sculptural remains thought to have belonged to the Romanesque cathedral or discarded in the successive restorations of the Gothic cathedral.