Johannes Kirchner was born in Reval (modern Tallinn, Estonia), then part of the Russian Empire and grew up in Saint Petersburg, where his father ran a school.
In 1880, he began studies in classical philology and history at Halle and Bonn under Hermann Usener and Franz Bücheler.
During his studies, he was a member of the Academic-Musical Association of Ascania Halle (part of the Sondershäuser Verband [de].
In addition to his educational work, Kirchner carried out research in the areas of Ancient Athenian epigraphy and prosopography.
His name is particularly associated with two great projects: the Prosopographia Attica (a collection of 16,000 short biographies of Athenians, mainly based on epigraphic evidence) and the second edition of Inscriptiones graecae II/III, a corpus of Athenian inscriptions from after 403/2 BC, much of which is still the standard reference work.