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.

Tomasz Raszkiewicz "forcibly lunged" at Lucasz Gal's mother as she held him in her arms, causing the baby to fracture his skull on a door.
Lucasz' "catastrophic" injuries mean he will have "no quality of life", Preston Crown Court heard.
Raszkiewicz, 33, admitted wounding or inflicting GBH with intent and was jailed for three years and two months.
The court heard Raszkiewicz was on the run from Polish authorities at the time of the attack on 22 November.
His name had not been included on Lucasz's birth certificate as part of his efforts to evade capture.
The court heard Raszkiewicz did not go to hospital with his son but left the couple's flat in Blackpool before his arrest three days later.
Sentencing, Judge Heather Lloyd told him: "You then lied and said this was a terrible accident. That was cowardly behaviour."
The court heard Lucasz's mother Jadwiga Gal gave the police five accounts as to how her son sustained his injuries, and it was the testimony of the boy's uncle which brought the case to court.
Judge Lloyd told Raszkiewicz his actions had resulted in "catastrophic, life-changing injuries".
"Such was the severity... a piece of his skull was embedded in his brain.
"He only survived as a result of the skill of the surgeons," she said.
The judge also criticised the boy's mother for choosing to protect Raszkiewicz rather than her baby boy.
"Lucasz will never life a normal life... and be dependent on others for the rest of his life," she said.
Raszkiewicz will be deported upon his release from prison, the court heard.
Det Sgt Chris Williams of Lancashire Police said Raszkiewicz had shown "no remorse" or "regard for the safety and welfare of this defenceless baby, who should have been safe in the arms of his mother".
Brazilian football star Neymar has appeared in court in connection with allegations of corruption and fraud surrounding his transfer to FC Barcelona.
[NEXT_CONCEPT]
A father whose drunken attack left his newborn son with severe brain damage has been jailed.