After failing the audition to join girl group Morning Musume with the fourth generation members, Fujimoto debuted as a solo artist within Hello!

After a successful performance on the music program on New Year's Eve, "Kōhaku Uta Gassen", producer Tsunku added her to Morning Musume as a sixth generation member in 2003.

[6] At this point in her career, she was given the nickname "Miki-sama" (美貴様、Miki the Great) by fans and the media alike due to her new image as someone who spoke her mind with a sharp tongue, even in the face of her seniors and instructors.

[8] She sang many of the lead lines in Morning Musume songs, especially after Natsumi Abe's graduation.

She and fellow Morning Musume member Asami Konno were also lent to Country Musume, a group that features "Country Girls from Hokkaidō", such as Miki and Asami (the group has been known, however, to include members not from the rural island—such as former featured singers Rika Ishikawa and Miuna Saito).

Up-Front Agency's initial response to the article was that they had no intention to deal with the situation since there was no proof of them dating.

Since she had no desire of ending the relationship, and she did not want to further betray the staff, fellow members, and her fans,[12] she decided the best course of action would be to immediately resign from the group.

[20] On April 23, 2008, Fujimoto released a collaboration kayōkyoku single, "Okitegami" (置き手紙, lit.

[22] In 2011, Fujimoto took part of the special revival unit Dream Morning Musume, though her concert and television appearances were limited, due to her concurrent pregnancy (with her first child).

[25] In 2017, Fujimoto appeared in the film Kamen Rider Ex-Aid the Movie: True Ending.

On March 12, 2023, in celebration of her 21st Debut Anniversary, Fujimoto held a 20 Complete Years[29] Anniversary Live Concert at Huric Hall Tokyo, featuring Asami Konno and Reina Tanaka as special guests, with surprise appearances by Maki Goto and Ichiro Ito (of Every Little Thing).