When he had finished education at the Lehrerbildungsamt in Kirchberg Theodor Werner studied beside his regular work at the Akademie Stuttgart under Robert Poetzelsberger in 1908-09. From 1909 to 1914 he stayed in Paris several times (for the sake of studying) and received a private education at the studio of Charles Guérin.
Following his military service Theodor Werner lived as a freelance painter in Großsachsenheim near Stuttgart until 1929. In 1930 he moved to Paris where he became member of the artists' group "Abstraction Création". One year later he married the woman painter Anneliese Rütgers, called Woty. After his return to Germany in 1935 Theodor Werner was banned painting and exhibiting and was regarded a "entarteter Künstler".
During the war he was pressed into service as an engineering draughtsman. During a bomb attack in the last year of the war the greatest part of his life work got destroyed.
The years 1946 to 1959 Werner spent in Berlin where he was member of the group "ZEN" from 1950 to 1955. A chair was bestowed upon him by the Akademie der Künste in Berlin. He became honorary member and finally honorary senator in 1956 at the Hochschule für Bildende Künste.
In 1959 Werner moved to Munich. Numerous national and international exhibitions and awards such as the Kunstpreis der Stadt Berlin (1951), the international award Lissone (Milan 1953) and the Kritikerpreis der Stadt Berlin (1954) testify for his acceptance.