The basic principle is that it is not prescribed to have two congregations in the mosque at the same time, because that is dividing the Muslims and they will disturb one another. But if there is a reason for that, such as the women not being able to hear the voice of the imam, then there is nothing wrong with having a separate congregation for the women with one of them leading them in prayer, when there is also a congregation for the men. But that is subject to the condition that the two congregations will not disturb one another.
It is proven that ‘Umar ibn al-Khattaab and ‘Ali ibn Abi Taalib (may Allaah be pleased with them) did that during Taraweeh prayers in the mosque, when they appointed an imam for the men, and another for the women.
Al-Albaani (may Allaah have mercy on him) said in an essay entitled Qiyaam Ramadaan:
It is prescribed for the women to attend it – i.e., Taraaweeh prayer – and it is permissible to appoint for them an imam of their own, other than the imam of the men. It is proven that when’Umar told the people to pray Taraweeh in congregation, he (may Allaah be pleased with him) appointed Ubayy ibn Ka’b to lead the men and Sulaymaan ibn Abi Hathamah to lead the women.
It was narrated that ‘Arfajah al-Thaqafi said: ‘Ali ibn Abi Taalib (may Allaah be pleased with him) used to enjoin the people to pray qiyaam (Taraweeh) during Ramadaan and he would appoint an imam for the men and an imam for the women. He said: I was the imam for the women.
I (al-Albaani) say: That is permissible, according to my understanding, if the mosque is spacious, lest they disturb one another. End quote.
And Allaah knows best.