In 1881 a Royal Order created a new parish division in San Sebastián. This new division included the creation of a parish, claimed for years by locals in the southern part of the city, which later became known as the "Ensanche of Amara". In August 1887 the City Council gave an area between the river Urumea and Beach of La Concha, occupied by sand dunes and marshes, to build the church. Until it was finished, the spiritual needs of the local congregation were met by a provisional parish, dedicated to the Sacred Heart of Jesus. Opened in March 1888, this rudimentary church was made of wood and was between Loiola and Príncipe Streets.

 The queen regent, Maria Christina of Austria, and her son, King Alfonso XIII, opened the church in 1897

In December 1887 a construction meeting chaired by the Dean D. Martín Lorenzo de Urizar Zalduegui-Ariño defined the bases of the project competition and set a budget of 750,000 pesetas, and like the capacity of the church and its architectural style, it should be pointed. Four projects were presented, with the chosen design being by the donostiarra architect Manuel de Echave, who was entrusted with the supervision of works. The new church would be dedicated to the Good Shepherd.

The Spanish royal family, who were vacationing in the city, were invited to the laying of the foundation stone. The events took place on September 29, 1888. The queen regent, Maria Christina, her children and the Infante Antonio, along with ministers and other officials, attended the solemn mass that the diocesan bishop D. Mariano Miguel Gómez held in the provisional parish church of the Sacred Heart. Following the ceremony, the royal entourage moved to the site of the new church and there proceeded to lay the foundation stone, which covered a lead box in which were enclosed pictures of the Pope and the royal family, various coins of the time and copies of the Gazette of Madrid and of the Ecclesiastical Gazette. The minutes of the ceremony were signed by the baby king Alfonso XIII, aged two years and four months, for which his mother had to take his hand. It is the first signature of Alfonso XIII on an official document.

Manuel de Echave went on to oversee the works having as master of the same José Vicente Mendía and, after his (Mendia) death, the master mason Agustín de Zumalabe. The foundation work required a careful drainage of the site to provide consolidated sand. For the general architecture the sandstone quarries of Mount Igeldo were chosen. The vaults were made with tufa from Ocio (Álava) and slate roofs were brought from Angers (France). The workers were all Basques.[citation needed] For the size of the stone of the capitals, ornaments, windows and needles that decorate the interior and exterior, the models presented by the local artist Julio Gargallo were accepted.

 View of the interior of the cathedral

After just nine years of work (including almost two in which work was suspended for lack of resources, and the tower was not yet crowned), the Church of the Good Shepherd was consecrated for worship on July 30, 1897. Again, the royal family, the Queen Regent María Cristina, King Alfonso XIII and the Infanta María Teresa attended the grand ceremony. The mass was officiated by D. Ramón Fernández de Piérola, Bishop of Vitoria, the diocese to which then belonged Guipuzkoa. The tower was completed in 1899 under the direction of Ramón Cortázar. In the end, the construction of the church cost more than 1,500,000 pesetas, and that was not including the altars and altarpieces.

Pope John Paul I's papal bull Quo Commodus of November 2, 1949, created the Diocese of Bilbao and San Sebastián seceding from the Diocese of Vitoria. The first bishop was the Catalan ecclesiastic Jaime Font i Andreu, appointed to office on May 13, 1950, and took office on September 3 that year. With the need to choose a Donostiarra church to host the local diocese, the choice was, by its magnificence and modernity, the Church of the Good Shepherd. On July 30, 1953, finally, the church achieved the rank of Cathedral with the consecration of the new altar, acting as pastor D. Ignacio Lasquibar Olaciregui, who in 1954 took over from D. Román Mendiguchia.

After four years of reforms and changes that were needed to put the church to its new use as a diocesan church. For this the presbytery was transformed with the installation of a new table after the removal of the original altar, of a florid Gothic style, carved in cedar wood by the Barcelonese workshops of Juan Riera, it was replaced by choir stalls and an image of the Good Shepherd. The Chapel of the Immaculate Conception was transformed into a chapter house, and the Chapel of Christ, in the crypt, became the new parish vestry, leaving the former sacristy for the exclusive service of the council.

In 1972, Bishop Jacinto Argaya Goicoechea undertook a second improvement of the church to mark the 75th anniversary of his inauguration. The neo-gothic pulpit made by Nicolás Medive, which was attached to one of the pillars, was removed. Also removed were the altars dedicated to Our Lady of Sorrows, Virgin of the Rosary and Virgin of the Pillar. The roofs and windows were restored and walls and vaults were cleaned. The old floor of American oak was replaced by a new one in marble. The interior lighting was improved and new benches were installed.