The Maputo Protocol was signed in 2003 by the African Union to protect women rights on the continent.
South Sudan has ratified the main African Charter's Protocol on Human Rights and the Rights of Women.
The South Sudan lawmakers ratified the protocol (with reservations) on Tuesday after length discussions.
Also known as the Maputo Protocol, the deal guarantees comprehensive rights to women, including the right to take part in the political process and the protection against Female Genital Mutilation (FGM) practice.
South Sudan's parliamentary committee for Gender, Child and Social Welfare and Religious Affairs, said the protocol was important in the fight against gender inequality in the war-torn country.
It also urged the government to launch a public awareness campaign to enlighten people on the protocol's importance.
Despite approving the protocol, the committee said there were some reservations.
They include an article which discourages polygamous marriages, another that guarantees the right of women to control their sexuality and to decide whether to have children, the number and the spacing, as well as the right to choose contraceptives.
Another reservation, the committee said, was the article that gives the right to procure abortion in cases of sexual assault, rape, incest, and where continuous pregnancy endangered the mental or physical health of the mother.
The committee, however, recommended that abortion could be permitted only in cases where pregnancy gravely endangered the life of a mother.
It also recommended that the abortion should be approved by a gynaecologist, adding that any abortion not approved by such an expert must be criminalised.
The Maputo Protocol was signed in 2003 by the African Union to protect women rights on the continent.
South Sudan becomes the 40th country to ratify the protocol out of the 54 African states.
