Lucimar da Silva asked for the leave two years ago when he and his partner adopted a child.
Brazilian law mandates that companies provide a four-month paid leave from work for a mother and five days paid leave for a father.
Silva argued it would be discriminatory to deny him the longer leave, noting the social security agency has already approved the four-month benefit for same-sex couples in which the partners are women.
An agency statement Thursday says the decision for da Silva does not set a legal precedent. It says all-male couples with adopted children will have to individually petition for the four-month leave.