Barcelona said it paid €57m (£43m) for Neymar in 2013 but investigators say the fee was closer to €83m and Barcelona concealed part of the deal.
Neymar spent an hour and a half before the judge.
He has previously denied wrongdoing, in an interview with Brazilian media.
Leaving court, the football star signed autographs for fans.
Barcelona FC says his parents, Neymar da Silva Santos and Nadine Goncalves da Silva Santos, received €40m and his former club, Santos, was paid €17m.
Neymar's father, who arrived at court with him on Tuesday evening, acts as his agent.
The case was brought by Brazilian third-party investment fund DIS, which owned 40% of the Brazilian player's sports rights.
DIS alleges it was financially harmed by the transfer when it received €6.8m of Santos's €17m fee and argues it was deprived of its full share.
Barcelona FC President Josep Maria Bartomeu and his predecessor, Sandro Rosell, were called to give evidence at the court in Madrid on Monday, but they refused to testify. They insisted instead on the version of events they had given at a previous hearing.
In a statement on Monday, the club said: "They are not worried and said they have confidence in justice."
The pair are also accused in a separate case of defrauding the Spanish tax office of an estimated €13m. They deny the allegations.
Neymar's move to Barcelona FC has been a big success on the pitch. The striker became part of a goal-scoring trio with Lionel Messi and Luis Suarez.
In 2015, Neymar helped the club win five trophies and came third in the Fifa Ballon d'Or competition. He also scored in the Uefa Champions League final against Juventus.
But the 23-year-old has also encountered legal difficulties in Brazil, where a court has frozen $47m (£33m) of his assets in connection with suspected tax evasion between 2011 and 2013.
Brazilian football star Neymar has appeared in court in connection with allegations of corruption and fraud surrounding his transfer to FC Barcelona.