The judges upheld lower court rulings that pay details are confidential, a spokesman said.
The woman, whom local media said is aged 46 and surnamed Oh, filed suit against the National Intelligence Service (NIS) in 2008.
She demanded that it disclose details of her husband's monthly pay, severance package and pension so that she could seek a divorce settlement.
"Information about NIS employees' pay is part of the agency's budget spending, which is defined as confidential under the National Intelligence Service law," the spokesman quoted the court's ruling as saying.
"The information should be kept confidential even if the disclosure request is made by a spouse."
Previous rulings have said the spy agency's spending should be kept secret even during parliamentary budget reviews, on the grounds that disclosure could be used to estimate the scale of its operations.
The agency, established in 1961 as the Korean Central Intelligence Agency and later renamed, collects information on matters related to national security including North Korean affairs.