Wagner's early work was in the already-established Neo-Renaissance style. In 1893 his general plan (never executed) for Vienna won a major competition, and in 1894 he was appointed academy professor.

As a teacher, Wagner soon broke with tradition by insisting on function, material, and structure as the bases of architectural design. Among his notable works in the Art Nouveau style are a number of stations for the elevated and underground City Railway of Vienna (1894–97) and the Postal Savings Bank (1904–06). The latter, which had little decoration, is recognized as a milestone in the history of modern architecture, particularly for the curving glass roof of its central hall.

Though much attacked at first, Wagner became widely influential. His lectures were published in 1895 as Moderne Architektur. An English translation appeared in The Brickbuilder in 1901.