Engler obtained a Ph.D. from the University of Breslau (now Wrocław) in 1866. After four years of teaching he became, in 1871, custodian of botanical collections of the Botanical Institute of Munich, remaining there until 1878, when he accepted a professorship at the University of Kiel. In 1884 he was appointed professor of botany and director of the botanical garden of the University of Breslau. From 1889 to 1921 he was director of the Berlin Botanical Garden, Dahlem, which he made one of the foremost botanical gardens in the world. He visited Africa in 1902, 1905, and 1913; India and Java in 1905; and in 1913 made a journey around the world.

Engler was a great administrator and the leader of German taxonomic and geographic botany. He collaborated with Karl Friedrich Philipp von Martius in the Flora Brasiliensis (1861–1906; “The Flora of Brazil”) and with Alphonse de Candolle in the Monographiae Phanerogamarum (1878–91; “Monographs of Flowering Plants”). His greatest contribution to taxonomy is his monumental Die natürlichen Pflanzenfamilien (“The Natural Plant Families”) edited with Karl von Prantl and others (published in parts, 1887–1911), followed by Das Pflanzenreich (1900–37; “The Plant Kingdom”). In these works, Engler provided a comprehensive system of classification whose arrangements of plant orders and families became widely accepted. Engler's Syllabus der Pflanzennamen (1892; “Syllabus of Plant Names”) is still a standard and indispensable reference book. He was also the founder of the Botanische Jahrbücher (“Botanical Yearbooks”), which he edited from 1880 until his death.