Weingartner was born in Zara, Dalmatia, which today is called Zadar in Croatia. His parents were Austrian. They were from a noble family. Felix had the title Edler von Münzberg. The family moved to Graz in 1868. His father died that same year. In 1881 he went to Leipzig to study philosophy, but soon spent all his time on music. He started his studies at the Conservatory in 1883. At the same time he studied with the great composer and pianist Franz Liszt in Weimar. Liszt helped him to get his first opera performed. In the same year, 1884, he became the director of the Königsberg Opera. He got conducting jobs in Danzig, then in Hamburg and in Mannheim. From 1891 he was Kapellmeister of the Royal Opera and conductor of symphony concerts in Berlin. Then he gave up that job and went to live in Munich.
In 1902, at the Festival of Mainz, Weingartner conducted all the symphonies of Beethoven. He was becoming famous in Europe as well as in the USA and in South America. From 1908 to 1911 he was the main conductor of the Vienna Hofoper, following on from Gustav Mahler. He kept the job of conductor of the Vienna Philharmonic until 1927. From 1912 he was again Kapellmeister in Hamburg, but in 1914 he went to Darmstadt. In 1919-20 he was conductor of the Vienna Volksoper. In 1920 he was Professor of the Franz Liszt Academy in Budapest. From 1927 to 1934 he was conductor of the Sinfonieorchester Basel. He gave his last concert in London in 1940 and died in Winterthur, Switzerland two years later.
Weingartner was married five times.
Weingartner thought of himself as a composer just as much as a conductor. However, it is as a conductor that he is remembered today. His compositions are hardly ever played now. He composed in a late-Romantic style, and he was an influence on the composer Erich Korngold. He is best remembered today as one of the great conductors of classical music, who conducted in a precise way without exaggerated effects. He wrote books about music including one about conducting.