Considering that he was also born from the collective sacrifice of all of earths shamans, I don't think real-life ages apply. B.C. could stand for "Battle of Catar" for all we know in a warhammer context.
If the emperor predated the birth of the dark gods in "reality" it would explain how he could learn so much about the warp without being effected by the influence of the gods.
So i would say he is ancient.
Chaos grew to significant power by the time of the rise of Slaanesh in early 30th (it's complicated because time doesn't exist in the warp). However Khorne the second oldest god is born somewhere in middle ages as far as i know and Nurgle predates him so i would say the Emperor must be born before Christs birth at least.