UFC officials confirmed the 170-pound bout to ESPN.com on Thursday. The UFC 189 pay-per-view will take place at the MGM Grand Garden Arena.
Ellenberger (30-9) will look to build off a second-round submission win against Josh Koscheck at UFC 184 in February. Based out of Southern California, Ellenberger had lost three consecutive bouts to Rory MacDonald, Robbie Lawler and Kelvin Gastelum before breaking the skid against Koscheck.
The 30-year-old welterweight is 9-5 overall in the UFC. Ellenberger told ESPN.com on Thursday he had originally agreed to a fight against Tyron Woodley, but the opponent was quickly changed to Thompson, who comes from a karate background.
"I've never turned down a fight," Ellenberger said. "One frustrating thing for me is that I got a call from [UFC president] Dana White, asking me to fight Tyron Woodley. I said, 'Absolutely, fantastic.' Next day, I hear, 'Well, he won't do it.' I never knew that was a choice. It's frustrating to me because that's the fight the UFC wanted.
"I'm not a bully. If he doesn't want to fight me, that's fine. But you claim you're the best in the world, prove it and beat anybody in the world. He likes to say I'm not on his level. He's lost to Jake Shields and Nate Marquardt, two guys I beat handedly. I'm not picking on him. I was just under the impression that was the fight."
Woodley (15-3) has publicly stated he wishes to fight former UFC champion Johny Hendricks.
"I just don't think a guy who is coming off three losses, who beats a guy who is also on a losing streak, is a legitimate opponent for me right now," Woodley said. "It's not like I'm trying to fight scrubs. The two guys I called out are a former champion in Johny Hendricks and a former title contender in Carlos Condit. I'm not reaching down, trying to get guys ranked lower than me. I've put myself in a position to fight for a title and really cash out on the time I've put into this sport. No disrespect to Jake, but he wants to be where I'm at right now. Nice try. I'm looking for Johny Hendricks."
Thompson (10-1) will take a four-fight winning streak into the fight. In his most recent appearance, Thompson scored a unanimous decision against Patrick Cote at UFC 178 in September.
"I've actually watched him quite a bit," Ellenberger said of Thompson. "He's got a very unique, interesting style. I got to train with some guys like Lyoto Machida for a few years, so it's something I've been exposed to in training over at Kings MMA. He brings something you don't really see these days and that's definitely interesting to me."