In a statement, the education ministry said scrapping the ban “is the first step in building a radically inclusive Sierra Leone where all children… are able to live and learn in safety and dignity”.
In 2015, Sierra Leone banned pregnant girls from going to school after a surge in sexual violence and teenage pregnancies driven by the Ebola crisis.
Women and girls in the former British colony face high levels of sexual violence, partly a legacy of the use of rape as a weapon during the civil war of 1991-2002.
Officials at the time of the ban argued that pregnant girls would be unable to learn and might influence other girls to get pregnant.
But the policy proved highly controversial.
Rights groups complained it was discriminatory and left teenage mothers chained to poverty as they were denied education.
In December, the Court of Justice of the West Africa bloc ECOWAS and ordered Sierra Leone to retract the ban.
“This doesn’t change the culture of violence against girls but it moves us in a big way in the right direction,” said Chernor Bah, the head of a local feminist organisation.
He added that successive waves of girls had been shut out of school and the impact of the policy would be felt “for many more years”.
On Monday, the education ministry said the decision to allow pregnant girls to attend school again wass effective immediately.
The announcement, however, comes as schools are set to shut from Tuesday in order to prevent the spread of