The Torah forbids a man to wear items of clothing which are exclusively ladies-wear (see Devarim 22.5). Sefer Divrei Malkiel proposes as an extension of the prohibition, that a boy not be given a girl's name.

[The commentators explain in many places, that the meaning of each name moulds the person (to some extent) who is named so. For example, one who is named Moshe will be given certain strengths (which he himself must develop) akin to those that Moshe Rabbeinu had. Presumably, a boy who is given a girl's name will have feminine tendencies – and this is what the Torah wishes men to avoid.]

Rav Chaim Kanievski shlita however, brings 65 examples of names of the Tannaim, Amaraim and Rishonim whose names corresponded to girls names.

In Sefer Melachim (b 15) the Navi mentions that Shalom ben Yavesh reigned as king of Yisrael for a month. The Midrash mentions a Rebbe Shalom, and Shalom ben Tikvah and Shalom ben Yoshiyahu are also mentioned by the Navi as being men.

The Gemara here tells a story concerning Rabban Gamliel and his sister Imma Shalom. We see from here, a clear proof that in the times of the Gemara the Rabbis were not concerned about unisexual names.             (See Taama Dikra p. 119 – 121)