It is the first of several cases against the combative 64-year-old leftist leader to go to trial.
A string of cases targeting Kirchner and her rival, current President Mauricio Macri, are clouding Argentine politics ahead of mid-term elections later this year.
Kirchner is accused of ordering the central bank to sell dollar futures at artificially low prices, causing Argentina to lose hundreds of millions. She denies wrongdoing.
Kirchner's defenders say she should not be prosecuted for a mishandled economic policy. But the accusation cited in the court ruling alleges that her and two other defendants' actions amounted to "fraudulent administration" of state funds.
He also called to trial Kirchner's former economy minister Axel Kicillof and Alejandro Vanoli, who was head of the central bank at the time, on the same charges.
A further 12 defendants face trial as alleged accomplices.
Kirchner faces separate investigations into alleged corruption. She has branded the probes politically motivated.
In the case now going to trial, Bonadio impounded a million dollars in Kirchner's assets last year.
She and her late husband and predecessor Nestor Kirchner had testy relations with Britain and the United States during their 12 years in power.
But Kirchner's court appearances during recent months of judicial investigation have brought her back to the public eye.
Crowds of supporters have rallied outside court in her support, reminding Argentina of her capacity to generate a media spectacle with those who still hail her as a champion of the poor.
The trial comes at a delicate time for Argentina, Latin America's third-biggest economy.
Mid-term legislative elections in October pose a test for center-right leader Macri, who succeeded Kirchner in December 2015.
Tens of thousands of striking teachers and other workers have staged mass protests against him in recent weeks.
One of his first moves after taking office was to devalue the Argentine peso.
That affected the worth of the state dollar investments made under the previous government.
Kirchner has alleged that businessmen who later became officials in Macri's administration themselves invested in the dollar futures in question.
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