He visited from 1947-49 the State Trade School, specializing in building construction, in Villach. After artistic controversies in 1949 he left both the Academy of Applied Arts and the Vienna Academy of Fine Arts. Initially influenced by the fantastic realism he got to know Jackson Pollock and Jean-Paul Riopelle in Paris and then turned to abstract microstructures in 1951.
In 1950 he found together with Ernst Fuchs, Anton Lehmden, Arik Brauer, Wolfgang Hollegha, Markus Prachensky, and Josef Mikl the ,,Hundsgruppe" with which he exhibited for the first time. In 1953 he began ,, overpainting" his own and other works. In the same year he met the Catholic priest Otto Mauer who found the Galerie St. Stephan, where he had his first solo exhibition in 1955. Wolfgang Hollegha, Markus Prachensky, Josef Mikl, and Arnulf Rainer found Painters Group ,, Galerie St. Stephan "under the direction of Otto Mauer in 1956. Religious themes determined his work in the years 1956 to 1957.
In the 1960s he began to paint pictures of his own body as well as illustrations of contemporary artists and old masters. At that time it was a social taboo, both in the field of eroticism and death masks. In 1977 he participated in the documenta 6, one year later, he represented Austria at the Venice Biennale. He was awarded the Grand Austrian State Prize ,, in appreciation of his work in the field of visual arts " in 1978. After a short period of hand and finger paintings he returned back to religious subjects in the 1980s. From 1981 on he was a member of the Academy of Arts Berlin and director of a master class for painting at the Academy of Fine Arts in Vienna. He received the Max Beckmann prize of the city of Frankfurt. A major exhibition took place in 1984 at the Centre Georges Pompidou in Paris.
The highlight of his career was the opening of the Arnulf Rainer Museum in 1993 in New York. In 1996 overpaintings of botanical and zoological illustrations from books of the 18th and 19th centuries, the series "leaf painting" and "microcosm" were created.
On the occasion of his 70th birthday the Stedelijk Museum in Amsterdam and the Art Forum in Vienna organized a large retrospective in Vienna. Since 2002 the Pinakothek der Moderne in Munich has been devoting a separate room to his works. In the following year, Rainer received the Rhenus Art Prize for his oeuvre. In 2004 Rainer became an honorary doctorate from the Catholic Theological Faculty of the Westfälische Wilhelms-Universität Münster and in 2006 he became an honorary doctorate of theology of the Catholic Theological Private University Linz.
In September 2009, the Arnulf Rainer Museum was opened in Baden near Vienna.
Most of the year Arnulf Rainer works on a farm in Enzenkirchen.
Overpainting is considered its own art form and made him internationally known as an Austrian artist of the postwar period.