Sources told the AFP news agency that she is the same missionary who was held for more than a week by Islamist gunmen in 2012 when the north had been taken over by groups linked to al-Qaeda.
On that occasion the woman was freed with the help of mediators from neighbouring Burkina Faso.
A French-led operation in 2013 drove Islamist fighters from northern towns.
A 12,000-strong UN peacekeeping force has now been deployed there, but militant groups are still active in the vast desert region.
Souleymane Maiga, a spokesman for the Malian army, told Reuters new agency that the Swiss national was taken from her house in the historic city on Thursday night.
A Timbuktu government official told AFP she was "Beatrice, a Swiss citizen".
Beatrice Stockly was seized by Islamist group Ansar Dine group in 2012.
According to AFP, two foreign hostages seized in 2011 by members of al-Qaeda in the Islamic Maghreb (AQIM), a South African and a Swede, are still in captivity.
Militancy in Mali
A Swiss woman has been kidnapped from her home in the northern Malian town of Timbuktu, security officials say.