The Seoul Administrative Court said it saw a "significant causal relationship" between the disease and even a low level of toxic chemicals because the worker Lee Eun-joo was exposed to carcinogens over a long period.
Lee died in 2012 after battling ovarian cancer for more than a decade. She worked at a Samsung chip factory for six years since 1993 when she was 17.
The court also blamed many night shifts and the factory's ventilation system. It ordered a government agency to compensate her family.
The court also said the agency should be less stringent in deciding eligibility for compensation when the cause of the disease is not completely clear cut.
In South Korea, a government agency levies companies and oversees insurance for workers with occupational diseases. Banolim, an advocacy group, says it has details of more than 200 current or former Samsung workers suffering from grave diseases such as leukemia. Of them, 76 have died. Less than a dozen cases had a causal relationship recognized by courts or the government.
