Jan Gebauer was born into a poor family in the small village of Úbislavice near the Giant Mountains.

Thanks to a recommendation from a local clergyman, Gebauer received an offer to study at high school in Jičín.

After his school-leaving exam, he first went on to study theology, but he did not finish it and enrolled onto a philosophy program at Charles University instead.

He received his Ph.D. in 1872 and became a docent of the Czech language at the Charles University in 1873.

In 1886, he exposed the Manuscripts of Dvůr Králové and Zelená Hora ("discovered" in 1817) as literary hoaxes by Václav Hanka in Masaryk's Athenaeum journal.