President Donald Trump's message came late on Sunday in a post on the Truth Social platform, where he praises Bongino as "a man with incredible love and passion for our country".
Both Bongino and the new FBI chief Kash Patel, who was approved by the Senate last week, are described as Trump-loyal. Patel has announced that he intends to reform the federal police FBI, including by placing greater emphasis on traditional crime-fighting tasks.
As deputy director, Bongino will be Patel's second-in-command on the post that traditionally is responsible for the daily crime-fighting operations.
Neither Bongino nor Patel has previously served within the FBI.