The decision overturns a ruling in July that said irregularities detected in the Brazilian's 2013 transfer to Barcelona were an issue for a civil court, not a criminal one.
Neymar's parents, Barcelona president Josep Maria Bartomeu and his predecessor Sandro Rosell – who resigned over the scandal in 2014 – also face corruption charges.
Both the defence and prosecution have 10 days to present their arguments before a final decision over whether the case will go to trial will be made, a statement from Spain's National Court said.
Should he be found guilty, Neymar, 24, faces a prison sentence of between six months and two years and a heavy fine.
Barcelona said Monday it would appeal the judge's decision, with which it expressed its “surprise and total disagreement… particularly given that the same magistrate decided to dismiss the case for all the defendants last July.”
According to the judge's findings, a pre-contract agreement between Neymar and Barcelona by which the player received €40 million ($44 million) in 2011 to ward off competing clubs for his signature “altered the free market of football transfers.”
Bartomeu and Rosell also stand accused of fraud over the transfer.
The case initiated with a complaint from Brazilian investment company DIS, which owned 40 percent of Neymar's sporting rights at the time of his transfer from Santos.
Barça initially announced the cost of the move at €57.1 million, 17.1 million of which was paid to Santos with the remaining 40 million paid to N&N, a company owned by Neymar's family.
However, Spanish authorities believe the real cost escalated to 83.3 million.
DIS received 6.8 million euros, 40 percent of the fee paid to Santos.
The company believe it was cheated of its real share because part of the transfer fee was concealed by Barcelona and Neymar.
Moreover, DIS also argued the pre-contract agreement between Neymar and Barça impeded other clubs from making offers for the player, affecting the value of the transfer fee.
The decision is another blow to the image of the Spanish champions and the player himself.
Barça hoped to bring an end to the murky affair when the club agreed to pay a €5.5-million fine in a deal with prosecutors in June to settle a separate case and ensure the club avoided trial on tax-evasion charges over the transfer.
Meanwhile, Neymar also faces tax evasion charges in Brazil.