"This child suffered a horrendous death at the behest of the armed opposition groups who currently control Kismayo," David Copeman, Amnesty International's Somalia campaigner, said in a statement.
Initial local media reports said Duhulow was 23, but her father told Amnesty International she was 13.
The Islamic Courts took control of much of Somalia in 2006, triggering an intervention by neighbouring Ethiopia, which propped up the UN-backed transitional government and ousted the movement.
While the group's political leadership largely fled the country, the movement's military and youth wing, the al-Shaabab, switched to guerrilla warfare.
In recent months the group appears to have gained strength, taking over the port city of Kismayo, and dismantling pro-government roadblocks.