Novák was born in Königgrätz (Hradec Králové), son of government officer Johann and Aloisia née Piperger.
He became interested in paleontology early in life thanks to the influence of his uncle Karel Feistmantel (1819–1885).
Around 1874 he studied the Silurian fauna along with Joachim Barrande and began to work along with Wilhelm Heinrich Waagen.
In 1887 he succeeded Krejčí as professor at the University of Prague but his health became bad in 1891 and he went to Italy to improve.
He began to study the paleolithic in quarry sites near Liteň while living with his sister who was married to Jan Wilt, the headmaster of the local school.