In light of Double AA's comment, if we consider a "yeshiva" as a school where young students are taught Gemara, there would come out a need for it to be separate gender from a purely academic (as opposed to social or herhorim) perspective.
Chazal tell us not to teach girls Torah in the Mishnah (sota chapter 3 Mishnah 4):
רַבִּי אֱלִיעֶזֶר אוֹמֵר, כָּל הַמְלַמֵּד אֶת בִּתּוֹ תוֹרָה, כְּאִלּוּ מְלַמְּדָהּ תִּפְלוּת.
Rabbi Eliezer says: whoever teaches his daughter Torah teaches her lasciviousness.
This is brought and refined in Shulchan Aruch Yorah Deah 246:6:
אשה שלמדה תורה יש לה שכר אבל לא כשכר האיש מפני שאינה מצווה ועושה ואע"פ שיש לה שכר צוו חז"ל שלא ילמד אדם את בתו תורה מפני שרוב הנשים אין דעתן מכוונת להתלמד ומוציאות דברי תורה לדברי הבאי לפי עניות דעתן אמרו חכמים כל המלמד את בתו תורה כאילו מלמדה תיפלות (פי' דבר עבירה) בד"א תורה שבע"פ אבל תורה שבכתב לא ילמד אותה לכתחלה ואם מלמדה אינו כמלמד' תיפלות (רמב"ם וסמ"ג ולא כמקצת ספרי הטור) : הגה ומ"מ חייבת האשה ללמוד דינים השייכים לאשה (אגור בשם סמ"ג)
A woman who studied Torah receives a reward, but not like that of a man, because she is not obligated yet performs the commandment. And even though she earns a reward, our rabbis have commanded that one should not teach his daughter Torah, because the majority of women are not intellectual prepared to be taught, and remove words of Torah to words of emptiness due to their intellectual limitations. The rabbis said: One who teaches his daughter Torah is as if he taught her frivolity. When is this stated? In regard to the oral Torah. However, in regard to the written Torah one should preferably not teach her, but if he did so it is not comparable to frivolity. Rama: Nonetheless, a woman is obligated to study laws that are relevant to her.
For a full treatment of this subject, see this answer.
I heard from Rav Yaakov Weinberg ztl (the Richmond Q&A )The following rule: if the girl wants to learn on her own, she can be taught whatever she wants, but the father cannot impress upon her to learn or know Torah Shebal Peh.
Assuming most students are not in yeshiva on a voluntary basis, the girls certainly can not be taught in the same way as the boys.