Wüllner was born in Münster and studied in his native place, and at Frankfurt, Berlin, Brussels, and Munich. Among his teachers was Anton Schindler, who styled himself Beethoven's amanuensis carrying on the true traditions of the master's style, a claim disputed by Beethoven's pupil Carl Czerny. In 1856 Wüllner became instructor in piano at the Munich Conservatory. He held the position of town musical director at Aix-la-Chapelle from 1858 to 1864. In 1867 he became director of the choral classes in the reorganized School of Music at Munich and wrote for them Chorübungen der Münchener Musikschule, text of score reading and singing (Solfege).
He succeeded the temperamental Bülow in 1869 as conductor of the Court Opera and the Academy Courts. Here he conducted the first performances of Rheingold and Walküre (1869, 1870) before the production of the entire Ring cycle at the first Bayreuth Festival of 1876. It is for these renditions that he is usually remembered now.
Among his works are: Heinrich der Finkler, a cantata for solo, male chorus, and orchestra; additional recitatives to Weber's Oberon, accepted by many of Germany's principal theatres; Psalm 125, for chorus and orchestra; Miserere for double choir; and Stabat Mater for double choir; besides masses, motets, songs, chamber music, and piano pieces.