Jocelyn and Ken Elliott, both in their 80s, were running a hospital in the West African country when they were taken by an al Qaeda linked group three weeks ago.
It's believed the couple had been held in neighbouring Niger.
A spokesman for the country's president said Mrs Elliot "was freed following mediation led by the president of Niger, Mahamadou Issoufou, and presented to the press this afternoon in Dosso."
He added that efforts to release her husband, who worked as a surgeon, were being intensified.
A statement released to Al Jazeera by al Qaeda in the Islamic Maghreb (AQIM) said the woman had been released because of guidance from its leaders "not to involve women in war".
The couple had been running a medical clinic in the town of Djibo for nearly four decades.
According to the Sydney Morning Herald Dr Elliot had once said: "We're meeting a need physically, but our ultimate aim is to show the love of God. The goodness and power of true medicine."