It is well-known that women are exempt from any Mitzvah which is time-bound (meaning any positive commandment that is assigned to a specific time, such as Tzitzit which are only worn during the day or Lulav which is only taken on Sukkot etc.) besides for certain Mitzvot which women are obligated to perform for special reasons, such as lighting Chanukah candles and hearing the reading of Megillat Esther which woman are obligated in for they were also part of those miracles. In general, however, women are exempt from time-bound Mitzvot. For this reason they are exempt from the Mitzvah of counting the Omer for this a positive commandment that is time-bound, for the Omer is only counted during a specific time of the year. Just like most members of the Jewish nation are exempt from Mitzvot pertaining to Kohanim and Leviyim, for most Jews are not Kohanim and Leviyim, similarly women are exempt from these kinds of Mitzvot since they were not commanded by Hashem to fulfill them.
Nevertheless, the Poskim write that there are certain Mitzvot that although women are exempt from, if they wish they may perform them, such as counting the Omer and the like. Such is the custom of many women that they perform the Mitzvah of sitting in the Sukkah as well as other time-bound Mitzvot, although they are exempt from these Mitzvot.
However, there is seemingly a question on this custom from the words of our Sages (Yerushalmi Tractate Shabbat Chapter 1, Halacha 2) that “if one is exempt from something and does it anyway, he is called a fool”. If so, it would seem that women should not fulfill Mitzvot that they are exempt from. This is especially difficult according to some of the great Rishonim including Rabbeinu Tam (Rosh Hashanah 33a), Ramban, Ra’ah, and others who have written openly that women may in fact perform Mitzvot which they are exempt from. It would seem that this contradicts the edict of our Sages that one who does so is considered a fool?
Maran Harav Ovadia Yosef Shlit”a writes to defend the opinion of the Rishonim with the words of the Meiri in his novellae on Tractate Rosh Hashanah (33a) who writes that the only time our Sages meant to dub someone who performs a Mitzvah he is exempt from as a fool is only when one performs a Mitzvah that everyone is exempt from. This is not the case regarding time-bound Mitzvot, which men are obligated to perform, and a woman is not considered foolish for performing them. (The Ramban and others write similarly.) It is thus understood why women may perform time-bound Mitzvot, for they are not performing Mitzvot which no one is obligated to perform, rather men are obligated to perform these kinds of Mitzvot.
We can deduce from here regarding the Mitzvah of counting the Omer that women are absolutely permitted to perform this Mitzvah if they please, just like other Mitzvot. However, they may not recite the blessing before counting the Omer, as we hold like Maran HaShulchan Aruch (Chapters 17 & 589) who rules that women may not recite a blessing over Mitzvot that they are exempt from, and if she does so, she is entering the realm of blessing in vain. (This is not so according to the Rama and the custom of many Ashkenazim that a woman may in fact recite a blessing on a Mitzvah that she is exempt from.)
In any case, we must note that according to the Mekubalim, it is preferable for women not to count the Omer at all, even without reciting a blessing, as there is a Kabbalistic reason for them to abstain from doing so. Therefore, our custom is that women do not count the Omer at all.