Directed by Head Coach Shane Murphy, USF's 2003-04 Men's Basketball Team finished 26-12 and was the first in school history to advance to a Final Four at the NAIA level. This team set a school mark for wins in a season with 26, finished the season with a GPAC Tournament title and won three games against nationally ranked opponents at the NAIA Tourney before falling to No. 2 Bellevue, 70-62, in the NAIA Final Four semifinals. The Cougars won 10 of their final 12 games to reach the NAIA semifinals.
Along with Murphy, now of Spearfish, SD, the coaching staff included current NBA Portland Trail Blazers Assistant Coach Nate Tibbetts, Midco Sports Analyst Brad Newitt of Sioux Falls, and current Dakota Wesleyan Head Men's Basketball Coach Matt Wilber. The Cougars, ranked No. 17 in the NAIA preseason poll, opened 3-0. After dropping to 4-2, the Cougars won 7-of-8 and moved to 11-3 overall. USF was ranked as high as No. 17 in the regular season. USF opened the GPAC tournament with a 66-60 win over No. 6 seed Concordia and then took a 73-68 decision over No. 2 seeded Morningside (ranked No. 22 nationally). At the NAIA National Tourney, USF opened with an upset by defeating No. 16 ranked Dickinson State, 85-67. In round two, USF pulled off another shocker by stopping No. 7 ranked Flagler College, 78-67. In the quarterfinals, USF took out its third straight ranked opponent by upsetting No. 21 Daemen College, 74-62. In the semifinals, USF fell to No. 2 ranked Bellevue (33-5). During the regular season, USF was 12-6 in the GPAC for third place. USF had a 14-6 nonconference mark and a 14-3 home mark. In the pre-conference slate of games, the Cougars, ranked No. 22 in NAIA DII, dropped an 88-77 decision to SDSU which was ranked No. 3 in NCAA DII, although USF led 37-35 at halftime.
In 2003-04, USF was led in scoring by Steve Esselink with 19.9 points per game (716 points) which ranked second in the GPAC and 22nd in NAIA. Esselink was named to the NAIA DII first team All-American Team and first team All-GPAC. USF had 12.3 points per game (466 points) and 8.8 (252) rebounds per game from JD Roberts, who led the GPAC in rebounding (23rd nationally) and blocks per game. Roberts was named to the NAIA All-Tournament Team and was second team All-GPAC along with senior forward Brett Moody, who averaged 10.8 points and 6.6 rebounds. Sophomore forward Chad Van Hill was honorable mention All-GPAC.
Team members included Beau Fitts, Troy Giegling, Jermaine Byrd, Chad Van Hill, Jeremy VanRoekel, Ryan Millsap, Steven Esselink, Jake Shaw, Dylan Kvaale, Paul McVey, JD Roberts, Eric Depue, Brett Moody, Matthew Begeman.