Investigating magistrate Pablo Ruz was already looking into whether Barcelona and former president Sandro Rosell avoided taxes which they should have paid in relation to Neymar's transfer in 2013.
Rosell, who has denied any wrongdoing, resigned last year over the allegations, saying he wanted to protect the club's image.
The probe began after a fan questioned the figures given by the club. Barcelona had additionally said they paid 57.1 million euros (43 million pounds) for the Brazilian forward but later backtracked and said the deal was nearer to 100 million euros.
Bartomeu will be questioned on Feb. 13 over whether Barcelona and their directors defrauded the Spanish tax office by 2.8 million euros in 2014.
The magistrate also gave club representatives five days to hand in tax documents relating to Neymar and to appear before him on the same day as Bartomeu.
He also ordered the Spanish tax office to provide tax returns and an additional report.
"In the last few months, Barcelona FC has asserted its innocence, providing all the documentation requested on numerous occasions," the Catalan club said in a statement on their website.
"The club has been advised all along by tax law specialists."
(Reporting by Sarah Morris,; Additional reporting by Rodrigo De Miguel, editing by Ed Osmond)
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