Karnavičius comes from a renowned family of musicians: his grandfather, Jurgis Karnavičius (1884–1941), was a composer, and his father, also named Jurgis (1912–2001), was a pianist and the long-time rector of the Lithuanian Academy of Music.
Karnavičius graduated from the Lithuanian Academy of Music in 1980, specializing in the piano.
Jurgis Karnavičius is a piano soloist who has played with different orchestras, and he often accompanies his wife, the opera singer Sigutė Stonytė.
In recent years he has been actively collaborating with several chamber ensembles, preparing concert programmes with the M. K. Čiurlionis String Quartet, Lithuanian Art Museum Quartet, Sostinės String Trio, and others.
In 2004, Jurgis Karnavičius earned a professorship with the Lithuanian Academy of Music.