Rudolf Eller (9 May 1914 – 24 September 2001) was a German musicologist and professor at the University of Rostock.
From 1934 to 1936 he studied organ, composition and choral conducting at the orchestra school of the Sächsische Staatskapelle Dresden, then until 1941 musicology, art history, history and philosophy at the universities of Leipzig and Vienna.
He began his professional career in 1945 with a position at the Musicological Institute of the University of Leipzig.
His teaching and research interests included Antonio Vivaldi and Johann Sebastian Bach.
Between 1971 and 1978 Rudolf Eller organized colloquia on Antonio Vivaldi in Dresden, and in 1979 a colloquium on Johann Sebastian Bach in Rostock.