Hundley, who missed 31 games on the disabled list earlier this season with a strained right oblique, is expected to miss between three and six weeks. The surgery will be performed in San Diego.
"It's pretty straight forward," Padres manager Bud Black said.
The Padres will add catcher Luis Martinez to their roster on Friday, and he's expected to be in uniform when the team opens a three-game series against Los Angeles at Dodger Stadium.
Martinez is hitting .313 with Triple-A Tucson.
"I had three options -- keep going, shoot the elbow up [with cortisone] and take a week to 10 days and see what happens or have surgery," Hundley said. "But the way that it's been going, there was no way of knowing if or when it would lock up on me."
Hundley missed four games last week with what the team called an irritated tendon in the elbow. He returned Friday to play in Seattle, but the pain in the elbow would come and go -- sometimes it felt fine, sometimes he couldn't bend it.
"There's times when it locked up when I was answering the phone or brushing my teeth," Hundley said. "There are some loose bodies floating around in there, some cartilage that we need to take out.
"If I knew it was going to get better, I'd play through it, but it's not getting better. And at some point, I'd be shut down because of it. I didn't think it was fair to the team if I kept playing."
Which is why Hundley, who is hitting .222 with three home runs and 15 RBIs over 153 at-bats this year, will have the surgery now, with the hopes of still returning this season.
"It's unfortunate, because he got off to a good start and then got banged up," said Padres catcher Rob Johnson, who will handle the primary catching duties with Kyle Phillips. "[Being injured] is a frustrating thing. But Nick has a positive spirit. He'll get through it."
Hundley said he first felt soreness in the elbow while catching against the Braves on June 25. He later had a cortisone shot and an MRI that showed no structural damage.