The indictment gives a green light for prosecutors to put Fernandez on trial. It states that the central bank colluded with the government ahead of elections in November 2015 to sell billions of dollars in currency futures at below-market rates.
Federal judge Claudio Bonadio said that the government had deliberately kept the Argentine peso inflated by selling dollars below market value and that this would not have been possible without Fernandez's approval.
It was "unthinkable" that a financial operation of this magnitude could have been executed without Kirchner's approval, he said.
Bonadio said this had cost the state about $5.2 billion (4.6 billion euros), allowing buyers to make big profits on the transactions. The sales also led to a sharp drop in central bank reserves. The charges refer to the end of Fernandez's second term in 2015.
Twelve other former officials were also charged, including former Economy Minister Axel Kicillof and former Central Bank President Alejandro Vanoli.
Fernandez was released on 15 million pesos ($1 million) bail. If found guilty, she could face a prison term of up to 20 years.
The transactions in the case involved between $5 billion and $17 billion, according to court papers published by Argentina's Judicial Information Center (CIJ).
Fernandez, who leads a large faction of the Peronist party, stepped down in December 2015 at the end of her second term.
Turning back a progressive agenda
During most of her eight years in office, Fernandez used a parliamentary majority to push through some progressive legislation. Argentina became the first country in Latin America to approve same-sex marriage, a universal child benefit plan was introduced, poverty was reduced, and pension funds were nationalized.
The move follows similar events in neighboring Brazil, where suspended President Dilma Rousseff faces impeachment over similar accusations of financial impropriety in office.
Corruption allegations were a permanent feature of Fernandez's eight years in the presidency. She has also been included in investigations involving allegations of money laundering.
Fernandez is thought likely to appeal the decision. She denied the charges and accused her successor, Mauricio Macri, and the justice ministry of "fabricating" the case as part of a personal vendetta.
Macri won the presidency on a platform of ending currency controls. Since they were lifted in mid-December, the peso has weakened by about 30 percent against the US dollar.
Macri, a center-right politician from the Cambiemos (Let's Change) party alliance, has said he intends to roll back many of the popular social-democratic elements of his predecessor's government.
jbh/jm (AP, dpa, Reuters)