Anti-government riots have occupied Istanbul for the past two weeks, but the tournament, which starts on June 21, has been given the green light by the governing body.
Istanbul is due to host 11 fixtures, including the final at Galatasaray's Turk Telekom Arena, but anti-government demonstrations in the city have prompted calls for the competition to be cancelled.
FIFA, however, has released a statement insisting it is still committed to hosting the tournament, with the decision coming after being assured the safety of those participating is not under threat.
"The riots deal with a domestic issue based in two contained areas in Istanbul," the statement read. "It is not foreseen that the tournament areas are affected. We are in contact with the Local Organizing Committee (LOC) and receive regular updates regarding the security situation.
"The LOC will continue its close co-operation with law enforcement and will regularly update FIFA. Safety and security is one of the most important matters in preparation of any major event. FIFA has full confidence in the Turkish authorities and their developed security concept for the Fifa U-20 World Cup which encapsulates any potential risks."
England, coached by Phil Taylor, have been drawn alongside Egypt, Iraq and Chile and could play in Istanbul if it reaches the quarterfinal stage, and the Football Association has given FIFA full control over safety fears. The United States is also in the tournament.
"We haven't made any extra security provisions for the team. This is FIFA's tournament and it will decide those matters," an FA spokesman told BBC Sport.