According to this source, women were not even allowed to be taught the Torah publicly in the Jewish faith, so they were not able to even sit in the same area as the men who were taught from the scriptures.
Restrictions applied to any public reading of Scripture in the
Synagogue (Megillot 73a) and they were unable to pronounce the
benediction after a meal in the home (Mishna Bereshit 7:2)....
This was practiced in the Second Temple period of Jesus’ time and in
synagogues afterwards; they were separated from men in the service.
This practice is continued today among Orthodox Jews. Although today
in most areas of Judaism (the reform side) much of this has changed
It is clear that Jesus challenged this trend in His public ministry. Even still, by the fourth century it appears that men and women were separated in churches, as St. Cyril of Jerusalem says,
Let men be with men, and women with women. For now I need the example
of Noah’s ark: in which were Noah and his sons, and his wife and his
sons’ wives. For though the ark was one, and the door was shut, yet
had things been suitably arranged. If the Church is shut, and you are
all inside, yet let there be a separation, men with men, and women
with women : lest the pretext of salvation become an occasion of
destruction. Even if there be a fair pretext for sitting near each
other, let passions be put away. Further, let the men when sitting
have a useful book; and let one read, and another listen: and if there
be no book, let one pray, and another speak something useful. And
again let the party of young women sit together in like manner, either
singing or reading quietly, so that their lips speak, but others’ ears
catch not the sound: for I suffer not a woman to speak in the Church.
And let the married woman also follow the same example, and pray; and
let her lips move, but her voice be unheard, that a Samuel may come,
and your barren soul give birth to the salvation of God who has heard
your prayer; for this is the interpretation of the name Samuel (Protocatechesis, 14,
NPNF, s. 2, v.7).
It is unclear if St. Cyril was instituting a new practice or affirming an existing one. It should be noted that many Coptic Orthodox continue the practice of sitting on separate sides of the church to this day. Many Anabaptists also have followed this practice. Various cultures practice this also. Some old churches still have matroneums from when this was practiced.
It should be kept in mind that the early Church suffered intense persecution until the Edict of Milan issued early in the 4th century under Constantine. It wasn't until this time that Christians were even able to construct buildings that were considered to be "churches." Prior to that, churches were assemblies (ecclesiae) of believers who gathered in homes to avoid being killed for their faith.