The National Court in Madrid ordered the trial of Barca's president Josep Maria Bartomeu, his predecessor Sandro Rosell and the club as a defendant in its own right.
They have always said they paid 57 million euros ($65 million) to sign the Brazilian star from his home club Santos in 2013.
The court suspects the actual price was 83 million euros and that Rosell and Bartomeu hid the real cost from the taxman.
Judge Jose de la Mata said in a written ruling there was evidence that they "knew the real cost of the signing of Neymar would be greater" than what they recorded in the club's 2013 accounts.
The defendants have 10 days to make court filings in their defence, the court said. It did not set a trial date for the time being.
The ruling comes as Barcelona aim for a possible treble in the Spanish league, Spanish cup and Champions League.
They knocked Bayern Munich out of the Champions League in the second leg of the semi-finals on Wednesday.