The Chosen One

The Chosen One is a significant trope in SF, and it's usually male.

Female Chosen One

The Chosen One ... is female.

Including works where a woman fulfills a prophecy, religious or heroic, or otherwise.

"Anamnesis" (Millennium episode 2x19) - a teenage girl who is having visions of the Magdalene, or the Virgin Mary
Gorman Bechard. The Second Greatest Story Ever Told (1991). God's latest kid is a girl.
Isobelle Carmody, Obernewtyn - Elspeth Gordie has a destiny ....
Suzette Haden Elgin Star Anchored, Star Angered - Drussa Silver is a messiah figure.
Elizabeth Hand Waking the Moon
Elizabeth Haydon Rhapsody
Elizabeth Haydon Prophecy
P. C. Hodgell Godstalk series: Godstalk, Dark of the Moon, Seeker's Mask - protagonist is one of a trinity; female is The Destroyer of the trinity
Elizabeth Kerner, Song in the Silence
Ursula K. Le Guin The Tombs of Atuan. Tenar, the protagonist, is The Eaten One, discovered via a Dalai Lama like search.
James Morrow Only Begotten Daughter. Another sequel to The New Testament, with a daughter. Deeply satirical.
Andre Norton and Sasha Miller. To the King a Daughter (2000)
Andre Norton and Mercedes Lackey. Elvenbane and Elvenblood
Midori Snyder New Moon (1989)
Midori Snyder Sadar's Keep (1991)
Midori Snyder Beldan's Fire (1993) (a quartet of novels about 4 women who fulfill a religio-political prophecy & free their people)
Sheri S. Tepper Singer from the Sea
Jane Yolen Sister Light Sister Dark

Sydney Bristow, "Alias" (term "chosen one" used in episode 3x11 "Full Disclosure"
Whale Rider (2002)

Gael Baudino -- some of her works, surely?
Clemen, James. WIT'CH series
Nicola Griffith Ammonite
Horwood, William. Second Duncton Wood series: Duncton Tales, Duncton Rising, Duncton Stone. But Privet doesn't fulfill a prophecy.
Robin McKinley The Blue Sword
Elizabeth Moon Paksennarion - fulfills a prophecy?
Terry Pratchett Equal Rites -- the 8th son of an 8th son turns out to be a daughter ... not exactly prophecied ...
Elizabeth Scarborough