The son of a court bailiff, Kefer was born in Axöd, then a hamlet, today a suburb of the city of Eggenfelden in Bavaria.

At the age of 10, he attended as a pupil and a chorister the Benedictine Asbach monastery, dedicated to St Matthew, near Rotthalmünster.

Initially without any financial support, but with electoral approval, Kefer founded a school on 18 August 1793 to train male trainees and journeymen in writing, reading and arithmetic in their free time alongside their professional work.

Shortly before his death, for his services to education, he became the Churfürstlicher und städtischer deutscher Schulinspektor (Electoral and Municipal German School Inspector).

Kefer created a Naturalienkabinett (Natural History Cabinet) for his schools to present types of wood and minerals for teaching purposes.

[1] The Bavarian ruler Maximilian I Joseph donated his tomb in Munich's Old South Cemetery (Burial Ground 3 - Row 1 - Place 32), with the following inscription: Max Joseph, Elector, honours the memory of Franz Xaver Kefer, founder and first teacher at the holiday school for artists and craftsmen in Munich with this monument.

He was followed by his wife Franziska, née Brandtl on 10 November 1851.Two reliefs on the monument could be reference to the 18-inch-high silver goblet award he had previously received in gratitude from masters and journeymen of the sword sweepers' and the cutlers' guilds in 1801.