Hunter says he's innocent and that he's excited to go to trial.
The Republican representative and his wife are accused of using more than $250,000 in campaign money on family vacations, dental work and other personal expenses.
They're also charged with concealing illegal spending in campaign records.
Hunter is seeking re-election this November and says the indictment has not changed that plan.
He claims the indictment is politically motivated.
"This is the new Department of Justice," Hunter said. "This is the Democrats' arm of law enforcement. It's happening with Trump and it's happening with me. We're going to fight through and win."
Hunter's opponent in the election, Ammar Campa-Najjar, released a statement on Twitter: "Today's indictment confirms just how deep this corruption can reach when someone like Duncan Hunter, Jr. is all in it for himself, instead of representing the people. Now is the time to put country over party."
I'll be on @FoxNews & @MSNBC today talking about what @Rep_Hunter's indictment means for the future.— Ammar Campa (@ACampaNajjar) August 22, 2018
Now's the time to put country over party. To explore unity, not exploit division. And fight against corruption.
As one voter said, "we don't need a Hunter, we need a gatherer." pic.twitter.com/xXKsk0VoBB
Meanwhile, the House speaker says Hunter will be removed from his committee assignments until this is resolved.