Haruko Obokata, 32, drew intense media scrutiny after failing to reproduce the results of what was once billed as a ground-breaking study on stem cells.
Last year Waseda University told her to correct her thesis, which it says contained copyright infringements and other flaws.
The university's president Kaoru Kamata announced the degree revocation yesterday after she missed an October 31 deadline.
Obokata reportedly opposed the revocation, saying she was considering bringing the case to court.
In January 2014 Japan's Riken Institute hailed Obokata's study into re-programming adult cells to work like stem cells.
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But doubts emerged about her papers on Stimulus-Triggered Acquisition of Pluripotency (STAP).
Mistakes were discovered in some data published in two papers, photograph captions were found to be misleading, and the work itself could not be replicated by other scientists.
Then Obokata herself failed to reproduce the successful conversion of an adult cell into a stem cell-like state, known as "STAP" cells.
The failure, which led to her resignation from Riken, marked a stunning fall from grace for Obokata, whose co-researcher committed suicide amid the scandal.
Riken later formally dismissed her study.