How should one who is menstruating pray istikharah?

It is prescribed for one who is menstruating, if she wants to pray istikharah, to offer the supplication of istikharah without praying (salah).

An-Nawawi (may Allah have mercy on him) said in al-Adhkar (p. 120): If a person is not able to pray, he may still recite the supplication of istikharah. End quote.

Shaykh Ibn Baz (may Allah have mercy on him) was asked: Is it permissible to pray istikharah without praying two rak‘ahs beforehand, or without wudu’? And is it permissible for the menstruating woman or woman who is bleeding postpartum to pray istikharah?

He replied: Yes, it is permissible to pray istikharah, it is mustahabb (recommended), and it is recommended to pray istikharah even without praying (salah) beforehand, because the person is asking of his Lord, and seeking guidance from his Lord, whether the person is a woman or a man, and whether the woman is menstruating or not. There is nothing wrong with any of that, but if it is done after praying (salah), that is better, because then it is praying istikharah in accordance with the Sunnah. So the individual should pray two rak‘ahs, then ask of his Lord, and ask his Lord for guidance, whether the person is a man or a woman. But if the woman is menstruating, or the matter is urgent, then one may pray istikharah without praying (salah) beforehand. There is nothing wrong with that, and he may ask of his Lord, praise be to Allah. Allah says (interpretation of the meaning): {Call upon Me; I will respond to you [Ghafir 40:60]. Istikharah is a supplication in which one turns to Allah for guidance."(Fatawa Nur ‘ala ad-Darb).

And Allah knows best.