Amina bin Abdulhalim Nassar was executed in the northern province of Jawf for "practising witchcraft and sorcery," the ministry said in a statement carried by SPA state news agency.
It is not clear how many women have been executed in the desert-kingdom, but another woman was beheaded in October for killing her husband by setting his house on fire.
The beheading took to 73 the number of executions in Saudi Arabia this year.
In September, Amnesty International called on the Muslim kingdom where 140 people were on death row to establish an "immediate moratorium on executions."
The rights group said Saudi Arabia was one of a minority of states which voted against a UN General Assembly resolution last December calling for a worldwide moratorium on executions.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's strict interpretation of Islamic sharia law.
Amnesty International says Saudi Arabia executed 27 convicts in 2010, compared to 67 executions announced the year before.