The 35-year-old Federer, seeded ninth, continued his dominant run through the tournament, ousting American Jack Sock 6-1 7-6 (4) in one of Saturday's semifinal matches.
No. 3 seed Wawrinka booked his spot in the final earlier Saturday by dispatching Pablo Carreno Busta of Spain in straight sets 6-3, 6-2.
Federer, in the finals here for the seventh time, has yet to lose a set or drop a serve in the tournament. He won the first set in 21 minutes before needing a tiebreaker in the second to close out the 21-seeded Sock and improve to 3-0 against the American.
"Overall I played a good match," Federer said. "In the second Jack got into it. I'm super happy to be in the finals."
Wawrinka reached the semifinals by winning consecutive three-set matches, but the three-time Grand Slam champion converted a pair of service breaks in the second set en route to winning in 65 minutes.
"It's an amazing result to be in the final here, especially in Indian Wells, one of the best Masters 1000," Wawrinka said. "I am really happy with the way I'm playing."
Wawrinka improved to 12-3 on the year, but one of those losses came at the hands of Federer in a memorable five-set match in the semifinals of the Australian Open.
"I have to be aggressive," Federer said of the looming final against Wawrinka. "I hope I can continue to play as well as I have."