Renho, a former model and TV anchor, took the reins of the Democratic Party (DP) last September in a landslide party election victory.
But her brief spell was dogged by controversy throughout and she was unable to capitalise on scandal-hit Prime Minister Shinzo Abe's falling popularity.
In particular Renho -- who goes by one name -- has been unable to shake off citizenship questions arising from her mixed Taiwanese-Japanese parentage.
It emerged just ahead of her election as party leader that she had never officially given up her Taiwan citizenship, even though Japan does not allow adults to hold dual nationality.
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Last week, she tried to put the matter to rest by showing official documents proving she now only has Japanese citizenship, but reportedly remained under fire within the party for mishandling the issue.
"I made the decision to resign," she said at a press conference Thursday, without offering specific reasons, though she said the citizenship controversy was not a factor in stepping down.
Her centre-left party -- formerly known as the Democratic Party of Japan -- swept to power in 2009, ousting the long dominant conservative Liberal Democratic Party (LDP).
Though still the largest opposition force, it has seen its position in parliament wane further, and was recently stung by a poor performance in local elections for the Tokyo assembly.
It has also been unable to take advantage of growing disapproval of Abe's ruling LDP, which has been hit by a series of scandals.
Renho first came to national prominence in the 1980s as a model and later TV newscaster, reporting from the earthquake- devastated city of Kobe in 1995.
She entered parliament in 2004, and sparked controversy six years later when she posed for a magazine shoot inside parliament for Vogue Nippon, the Japanese version of the international fashion monthly.