When is the best time to make the bracha upon washing one’s hand in the morning? There are a number of accepted answers to this question. The Mishna Berura (4), quoting the Magen Avraham, says that one should say the bracha only after one has washed his hands upon using the facilities. This is typically the second time that one has washed in the morning.
The Chayei Adam (and the Gra) write that one should delay the bracha until one has fully prepared for davening. The Beur Halacha has a lengthy discussion regarding this and offers an additional option of delaying saying this bracha until one is ready to say all the birkas hashachar, which can then be recited collectively.
Rabbi Shlomo Zalman Auerbach (see Ishei Yisroel chap. 2 note 105*) states that even if one knows that he will need to use the bathroom again before the beginning of krias shema, he nonetheless should say a bracha when he washes before davening.