Wegener, who was born in Berlin, was educated at the universities of Heidelberg, Innsbruck, and Berlin, where he obtained his doctorate in astronomy in 1905. In 1906 he went on his first meteorological research trip to Greenland and, on his return (1908), was appointed to a lectureship in astronomy and meteorology at the University of Marburg. After World War I he moved to a special chair of meteorology and geophysics at the University of Graz, Austria, in 1924. He made further expeditions to Greenland, where he died on his fourth visit.

In 1915 Wegener produced his famous work Die Enstehung der Kontinente und Ozeane (translated as Origin of Continents and Oceans, 1924), in which he formulated his hypothesis of continental drift. In this he proposed that the continents were once contiguous, forming one supercontinent, Pangaea, which began to break up during the Mesozoic Era and drifted apart to form the continents we know today.

To support his theory Wegener produced four main arguments. He first pointed to the obvious correspondence between such opposite shores as those of Atlantic Africa and Latin America. An even better fit was evident if the edges of the continental shelves were matched instead of the coastlines. Secondly he argued that geodetic measurements indicated that Greenland was moving away from Europe. This supported his third argument that a large proportion of the Earth's crust is at two separate levels, the continental and the ocean floor, and that the crust is made of a lighter granite floating on a heavier basalt. His final argument was that there were patterns of similarities between species of the flora and fauna of the continents.

Wegener's theory at first met with considerable hostility. However, in 1929 Arthur Holmes was able to suggest a plausible mechanism to account for continental movement and this, together with advances in geomagnetism and oceanography, was to lead to the full acceptance of Wegener's theory and the creation of the new geophysical discipline of plate tectonics after World War II.

Wegener's meteorological works include Die Klimate der Geologischen Vorzeit (1924; Climates in Geological Antiquity) published in association with his father-in-law, Wladimir Köppen.