The Justice and Equality Movement told the BBC it had been trying to protect children since the beginning of the seven-year conflict in Darfur.
The UN said children found in military areas or in conflict zones could be removed under the deal.
An estimated 6,000 children have been caught up in Darfur’s unrest.
The BBC’s Imogen Foulkes in Geneva said the UN children’s organisation was hailing the agreement, which took more than a year to negotiate, as a very valuable precedent which it hoped other rebel groups would follow.
Jem leaders, who have travelled to Geneva for the signing, said the movement had no child soldiers but that it was signing up to the agreement as a gesture of goodwill.
Fighting intensified in Darfur in May after Jem pulled out of peace talks with the government, accusing it of acting in bad faith.
The conflict between rebels and government-backed militias in Sudan’s western region is estimated by the UN to have cost the lives of 300,000 people and driven 2.7m people from their homes.