The female employee, who worked with a small children's nonprofit, was seized in the northern city of Gao on Saturday. There have been no claims of responsibility.
Malian officials said three men stormed the aid worker's home and took her and an orphan at the home in Gao, more than 1,200 kilometers (750 miles) from the capital, Bamako.
A local radio station in Gao said the victim was affiliated with "Aide Gao," a small aid agency that helps children suffering from malnutrition.
She was taken by a group of men who drove off in a Toyota pickup truck, the radio station said.
Hamadou Guindo, head of security for the governor of Gao, told The Associated Press (AP) that a rescue operation has been launched.
It was not clear who was responsible, or why the aid worker was taken.
The former French colony has been beset by attacks from resurgent Islamist groups like al Qaeda in the Islamic Maghreb (AQIM) this year, especially in the north.
Gao was occupied by Islamist extremists in 2012 until a French-led military operation forced them from power.
But United Nations peacekeeping patrols and Malian soldiers are still frequently targeted by attacks. However, kidnappings are rare.
Last month, the offices of the UN peacekeeping mission located next to the Gao airport terminal were razed by a truck-bomb explosion which forced the airport to close.
Another Swiss woman has been abducted twice by jihadists in the northern town of Timbuktu. She has been in captivity since her second kidnapping last January and is believed to be in the hands of al-Qaida-linked militants.
A French diplomatic source in Paris said it was trying to verify the information.
mm/kl (AFP, AP, Reuters)