Sandro Rosell has resigned as president of Barcelona with immediate effect.
Rosell made the announcement at a press conference on Thursday night following an extraordinary board meeting.
Rosell also named vice-president Josep Maria Bartomeu as his successor as president until 2016.
The decision comes after Spanish national court judge Pablo Ruz this week accepted a lawsuit that alleges Rosell misappropriated funds from the signing of striker Neymar from Santos last June.
Barcelona club member Jordi Cases has alleged that the amount paid was more than the €57million fee reported at the time.
"From the beginning I have said that the signing of Neymar Junior has been correct"
Explaining his decision to step down on Thursday, Rosell said: "For some time my family and myself have suffered threats and attacks in silence. These threats and attacks have made me wonder if being president means having to jeopardise my family.
"In recent days an unfair and reckless accusation of misappropriation has resulted in a lawsuit against me in the Audiencia Nacional.
From the beginning I have said that the signing of Neymar Junior has been correct and his signing has caused despair and envy in some of our adversaries.
"The right of the club members to be informed needs to be compatible with the defence of the club and confidentiality of certain matters and facts. This confidentiality is essential in the world of football because otherwise the club could be damaged.
"The board of directors is a team. And this team leads a project that has brought the club great success. I don't want unfair attacks to negatively affect their management or the image of the club. This is why I think my time here has come to an end.
"Now, in accordance with the club's statutes, I have presented my irrevocable resignation of the presidency of FC Barcelona to the board of directors."
The 49-year-old took over as Barca president in the summer of 2010 after winning a landslide vote to succeed Joan Laporta.
Rosell, who had been vice-president under Laporta before resigning in 2005, scooped 61.34 per cent of a record turn-out of 57,088 voters.
During Rosell's presidency, Barca have won two Primera Division titles, the Champions League, the Copa del Rey, the FIFA Club World Cup, the UEFA Super Cup and three Spanish Supercopas.