In 1883 the Holy See established the Apostolic Prefecture of Patagonia Meridional, Tierra del Fuego e Islas Malvinas, which was entrusted to the Salesian congregation.

In 1916, the prefecture was upgraded and its name changed to Apostolic Vicariate of Magallanes e Islas Malvinas, and on 17 January 1947, Pope Pius XII erected the diocese proper by means of the Bulla "Ut in amplissimo Patagoniae Chilensis territorio".

All the bishops of the diocese of Punta Arenas belonged to the Salesian congregation between 1916 and 2022.

Punta Arenas is the southernmost diocese in the whole Roman Catholic Church and its parish Nuestra Señora del Carmen, in Puerto Williams (Navarino island), is the southernmost Catholic parish in the world.

The mother church of the diocese is the Cathedral of El Sagrado Corazón (Sacred Heart) in the city of Punta Arenas.