Hellmesberger was born in Vienna and was the son of violinist and conductor Joseph Hellmesberger Sr. (1828–1893), who was his first teacher. Among his family of notable musicians were: grandfather, Georg Hellmesberger Sr. (1800–1873); uncle, Georg Hellmesberger Jr. (1830–1852); and brother, Ferdinand Hellmesberger (1863–1940).

In 1875 Hellmesberger became a member of his father's Hellmesberger Quartet, while in 1891 he became leader. In 1878 Hellmesberger became solo violinist of the Vienna Court Chapel and professor at the Vienna Conservatory. In 1890 he was the first hofkapellmeister at the Vienna Court Opera, and from 1901 to 1903 he was principal conductor of the Vienna Philharmonic.

In 1904 and 1905 he was Kapellmeister at the Stuttgarter Hoftheater

His compositions include 22 operettas, 6 ballets, dance music and lieder.

Hellmesberger died of kidney failure, in Vienna at age 52.

• Free scores by Joseph Hellmesberger Jr. at the International Music Score Library Project (IMSLP)
• Josef Hellmesberger Jr. biography at the Tribal Smile Music Encyclopedia
• Josef Hellmesberger Jr. biography Archived 2008-01-06 at the Wayback Machine at aeiou Encyclopedia
• Biographies of members of the Hellmesberger family (in German)