The younger Mr Biden is accused of lying about his drug use when he purchased a firearm in October 2018. He has acknowledged that he struggled with drug addiction during that time.
It is illegal in the US to purchase firearms while addicted to a controlled substance.
Mr Biden was indicted after a plea deal concerning gun and tax charges with federal prosecutors fell apart over the summer.
Republicans at the time had insisted Mr Biden was getting a sweetheart deal and pointed to a double standard, contrasting the treatment the President's son was receiving to the many investigations into former president Donald Trump.
Mr Biden's indictment was brought by special counsel David Weiss.
He could also face tax charges in Washington or California, where he lives.
Congressional Republicans are looking to link the younger Mr Biden's business dealings to the President's through an impeachment inquiry. Thus far, no evidence has shown that the President has abused his power.
The younger Mr Biden has gone on the offensive in recent weeks, suing Trump lawyer Rudy Giuliani and another legal representative for sharing his personal data after obtaining it from a computer repair shop. He also filed a lawsuit against the IRS.
He is charged with two counts of making false statements and an additional count of illegal gun possession.
He could face up to 25 years in prison if convicted.