Morningside (10-1) is appearing in the quarterfinals for the eighth time in the last 10 seasons, while Baker (11-1) qualified for the round for the first time since 1993 – seventh overall.
The Mustangs won the two sides' only previous playoff meeting with a 65-27 victory in the 2008 first round.
Baker, who is hosting its first quarterfinal game since 1993, is 5-1 all-time in the quarterfinals, while Morningside is 2-5.
Since 2000, the home teams in the FCS quarterfinals are 39-12 overall, with home teams going 4-0 last season.
Morningside defeated No. 10 Rocky Mountain, 40-21, at home in the first round of the NAIA FCS game on Saturday to move on to the quarterfinals, while the Wildcats took down No. 13 Sterling, 10-7.
The Baker University athletic department will provide live stats and live video for the game on Saturday, for more information please visit www.bakerwildcats.com.
2013 NAIA Football Championship Series Quarterfinal Pairings
Game 1: Saint Francis (Ind.) (9-2) at Cumberlands (Ky.) (11-0), TBA
Game 2: Tabor (Kan.) (10-2) at Grand View (Iowa) (11-0), TBA
Game 3: Missouri Valley (9-2) at Carroll (Mont.) (11-1), TBA
Game 4: Morningside (Iowa) (10-1) at Baker (Kan.) (11-1), TBA