Old English, from Late Latin amen, from Ecclesiastical Greek amen, from Hebrew amen "truth," used adverbially as an expression of agreement (as in Deuteronomy xxvii.26, I Kings i.36), from Semitic root a-m-n "to be trustworthy, confirm, support."
Compare similar use of Modern English certainly, absolutely. Used in Old English only at the end of Gospels, otherwise translated as Soðlic! or Swa hit ys, or Sy! As an expression of concurrence after prayers, it is recorded from early 13c.