Waldteufel was born to a family of musicians; his Bavarian mother was a pianist, and his father was a violinist and dance composer. The family moved from Strasbourg to Paris in Waldteufel's early childhood, and while young Emile studied piano privately, he did not enroll in the Paris Conservatory until he was 16 (Massenet was one of his fellow students). There his emphasis remained on the keyboard, but he dropped out before receiving his diploma. Waldteufel supported himself as a piano tester for the manufacturer Scholtus, while also giving lessons and playing at private soirées.

With his father's orchestra popular in high society, Waldteufel managed in 1865 to land an appointment as court pianist to Napoléon III; he began conducting state balls the following year. He had already written a few dances (he published his first waltz at his own expense in 1859), but he became much more active as a composer from this time, especially after his service in the Franco-Prussian War. Manola, from 1873, was his first international success; he works from later in the 1870s are still recorded with some regularity, and his greatest hit, Les Patineurs (The Skaters), came in 1882. His later pieces are less enduring, but during the last phase of his career Waldteufel performed in London and Berlin besides presiding over the most fashionable and important balls in Paris, notably the presidential balls. He retired in 1899, coincidentally the same year that Johann Strauss II died; Waldteufel lived until 1915.