In 1956, the Government of Navarre established the Museum of Navarre as a separate entity. It can be found in Pamplona's Old Quarter on Calle Cuesta de Santo Domingo s/n. Its chapel and façade are 16th-century artefacts.

Only the main façade and the chapel interior remain of the former Nuestra Seora de la Misericordia hospital, which was established in the sixteenth century.

The façade is the unique specimen of Renaissance civil architecture in Pamplona, and it was created in 1556 by Juan de Villarreal and Martn de Azcárate. It is a reinterpretation of the triumphal arch from ancient architecture with a wide range of Plateresque-inspired ornaments.

A 17th-century altarpiece from a church that once stood in Calle Mayor, across from Santiago Church, in Puente la Reina, serves as the façade of the chapel's side entrance. Juan de Ancheta constructed the chapel, which is now a part of the museum and is being utilised as an auditorium, between 1547 and 1550 in the Gothic-Renaissance style.

The hospital was relocated to the Hospital de Navarra in 1932, and José Yarnoz Larrosa renovated it in 1952 to turn it into a museum, preserving almost nothing of the original Renaissance structure.

The museum underwent a redesign in 1986 by architects Jordi Garcés and Enric Soria to modernise and restructure it. Only the most significant pieces were displayed during this reorganisation, providing greater room for their study. By adding a gathering space, a space for temporary exhibits, and other amenities, the museum was intended to be more accessible to the general public. The prehistoric artefacts were placed in a new room under the garden, the Roman mosaics were displayed in various locations on the ground floor, and the remaining items were spread out over four stories.

Set against a blind wall, the Renaissance façade stands out as a distinctive aspect of the museum.

The artwork was compiled by the Commission of Historical and Artistic Monuments of Navarre, which was established in 1860, and was followed up on in 1940 by the Prince of Viana Institution, an agency of the Navarrean government, with the aim of safeguarding, restoring, and researching the region's artistic and archaeological heritage. There are significant Roman artefacts there as well as a Goya picture.