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 57 million euro (£48.6m) fee reported at the time.
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.
Agusti Benedito came second, with just 14.09 per cent of the vote followed by Marc Ingla (12.29 per cent) and Jaume Ferrer (10.80 per cent).
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.
Rosell added: "In these four years we have enjoyed and suffered because we are Barcelonistas, just as many generations of Blaugranas have enjoyed and suffered for more than a century.
"In all of these years we have seen that our successes are the result of our victories on the pitch and overcoming innumerable obstacles off the pitch: political, external and, what's worse, at times the pressure has come from our own environment
"It has been an honour to serve the Barcelonistas. It's been a privilege to be the president of FC Barcelona."
During the press conference, which was delayed by over an hour from its original scheduled starting time while the board meeting continued, Rosell confirmed Bartomeu as his replacement.
Rosell said: "The first vice-president of the club, Josep Maria Bartomeu, will immediately assume the presidency of the club until the end of the term, through 2016, just as the board unanimously agreed a few moments ago.
"I wish the best to the new president and I ask the club members to support him."
Bartomeu, who was sat alongside Rosell, said: "My first desire is to announce the continuation of the board's project until 2016.
"I ask the club members for their support. I encourage them to continue to have confidence in this project."
Barca, who last season won their fourth Primera Division title in the last five years and 22nd in their history, are currently joint top of La Liga with Atletico Madrid on 51 points.
They are through to the last 16 of the Champions League, where they will face Manchester City, while they are on course to reach the last four of the Copa del Rey after earning a 4-1 lead from the first leg of their quarter-final tie with Levante.