Boykin overcame a 7 of 16 first-half performance by completing seven of his first nine passes in the second half, tossing touchdown passes of 20 and 56 yards to help the Horned Frogs (2-2, 0-1 in Big 12) overcome a 10-7 halftime deficit.
The Horned Frogs retain the Iron Skillet trophy for the second straight year, and they are 11-2 under coach Gary Patterson in the annual rivalry game.
SMU (1-3), which entered the game 10th in the nation in passing, amassed 292 yards of total offense, and quarterback Garrett Gilbert finished 23 of 44 for 276 yards and four interceptions. TCU also had six sacks, its most since 2009 at Virginia.
TCU played without star defensive lineman Devonte Fields, who was out with an unspecified injury.
Without Fields, the 2012 Big 12 Defensive Freshman Player of the Year and Freshman All-American, the TCU defense struggled to get much rush on Gilbert early on, but it bottled up the middle of the field. SMU's running backs combined for just 18 yards on 10 carries in the first half.
TCU's defense stepped up in the second half, forcing six straight incompletions from the former Texas starter and picking up the pass rush. After TCU tied the game at 10 thanks to a 35-yard Jordan Oberkrom field goal, Gilbert's was intercepted by Sam Carter and returned 25 yards to the SMU 32.
After driving inside the 10 following the interception, the snap went through the legs of Boykin to set up a third-and-18 from the 20, but the sophomore quarterback found Ty Slanina in the left corner of the end zone to put the Frogs up for good.
Boykin led five straight scoring drives in the second half, which included a 6-yard touchdown run by B.J. Catalon with 10:33 left in the fourth quarter to give TCU 31-10 lead.
After SMU cut the lead to 35-17 with 3 minutes left in the game, Ladarius Brown returned an onside kick 45 yards for a touchdown, and Carter returned his second interception of the game 66 yards for another score.
The Frogs came into Saturday's game after a much-needed bye week, following a sluggish offensive display against Big 12 rival Texas Tech on Sept. 12 in Lubbock, Texas.
Saturday's first-half edition of the Frogs' offense showed little improvement during the 16-day break, and fans began booing the Frogs after they went four possessions without a first down in the second quarter, which included a missed 42-yard field goal after an SMU fumble in its own territory.
The boos quickly turned into groans as the Frogs stalled at their own 10-yard line late in the second quarter, and Ethan Terry's punt was deflected by Jackson Mitchell close to the end zone. The ball sailed to the 11 and was picked up by Ajee Montes, who returned it to the 1.
Fortunately for the Frogs, SMU's offense fared no better in the opening half. After Prescott Line was dropped for a loss of 1, Gilbert fumbled a low snap and although the Mustangs recovered, SMU had to settle for a 34-yard field goal by Chase Hover with 58 seconds left in the half.
SMU took a 10-7 lead into the half after limiting the Frogs to just 120 offensive yards, while TCU held the Mustangs to minus-16 yards rushing on 17 carries. K.C. Nlemchi led SMU on the ground with 10 carries for 46 yards rushing, nine of the touches coming in the second half.
The Mustangs opened the scoring with a 1-yard touchdown pass from Gilbert to Jeremy Johnson with 4:41 left in the first quarter. Johnson led SMU with 10 catches for 149 yards.
James Waymon, who led TCU with 54 yards rushing on 11 carries, scored from 2 yards out 9 seconds into the second quarter to make it 7-7.