The club was founded on May 14, 1966, when the amateur clubs
Unión Bellavista and
Portuario Atacama merged. The team's original name was
Club de Deportes Antofagasta Portuario. The team's first manager was
Luis Santibañez, future manager of the
Chile National Team. The team finished 10th in its first league season. Under coach Francisco Hormazábal, Antofagasta was crowned champions of the second division in 1968. The final was played on January 19, 1969, against
San Luis. The only goal of the match was scored by the Paraguayan player Juan Pelayo Ayala. The team was promoted to first division after that game. On July 21, 1974, the team changed its name to
Club Regional Antofagasta. In 1977, the team finished 18th in the table and returned to the second level. In 1979, Jorge León was named the team's president and changed the club's name to
Club de Deportes Antofagasta. The
regional was not appropriate anymore, because a second team,
Cobreloa, had been established in the
Antofagasta Region. On June 30, 1983
D. Antofagasta, coached by Manuel Rodríguez, returned to the top level once after defeating
Lota Schwager 9–0. However the following year the team was again relegated. D. Antofagasta experienced one of their most successful spans from 1991 through 1995, playing in the top tier under the guidance of
Croatian coach Andrija Perčić, with star players such as
Marco Cornez and
Gabriel Caballero. In 1997, they once again descended to the second level, after finishing at the bottom of the table. In 2005, D. Antofagasta gained promotion to the first division along with
Santiago Morning. In 2008, the club returned to the Primera B, finishing at the bottom of the cumulative table 2007–08. In 2011, they won the Primera B championship and were promoted to the Primera Division. ==Stadium==