Wray, 50, received a bipartisan support of 92-5 votes on the Senate floor.
"The FBI is our country's top law enforcement agency and it needs a qualified leader committed to upholding the rule of law and protecting its independence. I'm confident that Christopher Wray is up to that considerable task," Senator Dianne Feinstein, Ranking Member of the Senate Judiciary Committee said.
"He said he would resign if President Trump asked him to do anything illegal, and that he would consider any effort to tamper with Special Counsel Robert Mueller's investigation to be unacceptable," she said.
Mueller's team is investigating Russia's interference in the 2016 presidential election.
A former high-ranking official in President George W Bush's Justice Department who oversaw investigations into corporate fraud, Wray takes up the top job at a critical juncture marked by the ouster of Comey, 56.
Trump on May 10 abruptly fired Comey who was overseeing a criminal probe into whether the Trump campaign colluded with the Russian government to influence the 2016 presidential election that was won by the real estate mogul.
Senate Democratic Whip Dick Durbin said the next FBI Director will be under incredible scrutiny.
"America needs an FBI Director who will face that pressure with integrity, independence, and a firm commitment to the rule of law. He may also have to stand up to this President if the interests of justice demand it. I believe Mr Wray can do that, and Congress will be closely monitoring the FBI to ensure Mr Wray is effectively serving the American people and the rule of law," Durbin said.
Wray is a proven public servant with an impressive law enforcement track record, and he is well-equipped to take the reins of the FBI during these challenging times, Senator Tom Carper said.
In a statement, Senator Ben Cardin, Ranking Member of the Senate Foreign Relations Committee, said Trump's firing of Comey and his continuing public criticism and intimidation of Attorney General Sessions and Deputy Attorney General Rod Rosenstein shows that "the President has little respect for the rule of law or separation of powers".
"Mr Wray will have a steep challenge ahead of him as he swears to support and defend the Constitution," he said.
Cardin said it is outrageous that the Trump administration's decision to cancel the current request for proposals for a fully consolidated FBI headquarters puts America's national security at risk.
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