Alongside his diplomatic career, Henri Pognon engaged in Mesopotamian archeology in Lebanon, Syria, and Iraq.
Combining field discoveries, acquisitions from local scouts and official prospecting missions, he collected Semitic inscriptions whose meaning he penetrated through an intense translation work.
In 1883 he discovered two important inscriptions on bas-reliefs from the reign of Nebuchadnezzar II in the Wadi Brissa in Lebanon.
He produced a pioneer work with his publication in 1898 on the Mandaic incantation bowls from Khouabir, a cemetery site near the bank of the Euphrates southwest of Baghdad, which was proceeded by the first published Mandaic bowl from Adab (Tell Bismaya).
His collection of Syriac manuscripts, gathered in Aleppo and Mosul, is the origin of much of the Graffin funds which in turn joined the Bibliothèque nationale de France in 1989.