Little is known about his youth, but he grew up in a musical family; his brother Peter Albrecht Hagen (also called Peter Albert van Hagen, 1714 - 12 September 1777) studied the violin with Francesco Geminiani, learned to play the lute and organ, and was an organist in Rotterdam.
The younger Bernhard Joachim Hagen must have learned to play lute and violin early too, for in 1737 he was already employed as an assistant to Bayreuth violin virtuoso and Kapellmeister Johann Pfeiffer; later he was listed officially as a court violinist.
There is a clearly discernible influence of Carl Philipp Emmanuel Bach in Hagen's music.
There are 33 known compositions by Bernhard Joachim Hagen found in the Staats- und Stadtbibliothek Augsburg: The facsimile editions of Hagen's solo lute sonatas (1983) and chamber works (1984) have been published by Joachim Domning for the Roman Trekel Musikverlag.
The lute sonatas of Roman Turovsky-Savchuk (a contemporary lutenist-composer) were written in homage to Hagen.