Schimper was born at Strasbourg, which is now in France. He first became interested in natural history while on excursions with his father, Wilhelm Philipp, who was professor of natural history and geology at the University of Strasbourg. Andreas entered the university in 1874, obtained his doctorate in natural philosophy in 1878, and in 1880 earned a fellowship to Johns Hopkins University. He returned to Germany in 1882 and became lecturer and eventually professor at the University of Bonn (1886), where he remained until in 1898 he was appointed professor of botany at the University of Basel.

While at Strasbourg Schimper made an important study of the nature and growth of starch grains showing that they arise in specific organelles, which he named chloroplasts. However, it is to the study of plant geography and ecology that he made his most significant contributions. During travels to the West Indies in 1881 and 1882–83, Brazil (1886), Ceylon (Sri Lanka) and Java (1889–90), and the Canary Islands, Cameroons, East Africa, Seychelles, and Sumatra (1898–99) with the Valdivia deep-sea expedition, he made ecological studies of tropical vegetation. His results led to publication of important papers on the morphology and biology of epiphytes and littoral vegetation, culminating with his masterpiece, Pflanzengeographie auf physiologischer Grundlage (1898; Plant Geography Upon a Physiological Basis), which relates the physiological structure of plants to their type of environment.