The woman, whose name was not given, was 15 when the government forced her to undergo a sterilisation procedure in 1972 after she was diagnosed with a mental disability, local media reported.
She is reportedly seeking 11 million yen ($100,000) in damages, saying the state failed to offer relief measures while seriously violating her human rights under the law which remained in force until 1996.
The lawsuit was filed on Tuesday, a court spokesman told AFP, declining to give further details. The plaintiff's lawyer was not immediately available for comment.
Some 16,000 people were forcibly sterilised under the notorious eugenics law, according to the Japanese bar association.
"We've had agonising days... we stood up to make this society brighter," the woman's sister-in-law said at a televised press conference.
Asked about the lawsuit, Health Minister Katsunobu Kato declined to comment, saying he was not aware of the details of the case.
Children as young as nine were forced to undergo the procedure, according to the Mainichi Shimbun.
Germany and Sweden had similar eugenics laws and governments there have apologised and paid compensation to the victims.
Under Japan's eugenics law, some leprosy patients were also forced into abortions because of policies that forbade them from having children.
In 2005 a Japanese court for the first time ordered the state to pay damages to a former leprosy sufferer affected by the law.
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