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Conference membership

• 1913: Independent
• 1914–1996: Southwest Conference
• 1997–2005: Western Athletic Conference
• 2006–present: Conference USA

Southwest Conference (1914–1996)

In 83 years of Southwest Conference play, Rice finished in the bottom half of the conference in 72 times. Rice finished in last place for 24 of those seasons. The highest Rice rankings in SWC regular season play were second-place finishes in 1984 and 1994.

The Wayne Graham Era (1992–2018)

The modern era of Rice baseball began in 1992, when Wayne Graham, who had previously led San Jacinto College to five junior college championships, became head coach. Graham has coached 27 different players to All-America honors. In 1995, Rice finally broke through to make the first NCAA tournament appearance in school history--the first of 20 consecutive tournament appearances, including seven College World Series.

A year later, Rice won the 1996 Southwest Conference baseball tournament, the final SWC tournament. It would be the first of 19 consecutive regular-season or tournament titles in three different conferences.

Recently, Baseball America ranked Rice as the best baseball program in a nine-year survey of all 293 Division I programs since 1999. Data cited in the survey included Rice's five College World Series appearances and 2003 championship, its 35 major-league draft picks, and its 15 All-America selections over that span. Graham whose 953 victories over 21 seasons make him both the winningest and longest-tenured coach in Rice history.

2003 National Championship

We're only a step away from being the capital city of the capital state of the baseball world. This is going to be the greatest baseball city in the country and the world... I want Rice University to be Houston's team.

— Owls head coach Wayne Graham in 2003

Rice entered the 2003 postseason having won 30 consecutive games early in the season and having won the WAC regular-season championship. The team had a 3–0 record in the regional round, defeating McNeese State once and Wichita State twice at Reckling Park to advance to the super regionals. In the super regionals, Rice faced off against cross-town rival Houston. In the regular season, Rice had beaten the Cougars in four of five games. After losing the first game 5-2, Rice rallied to win the second game 10–2 behind four home runs, including a three-run homer by Vincent Sinisi. Rice advanced to their second consecutive College World Series by winning 5–2 in game 3.

Rice entered the 2003 College World Series with a starting rotation made up of three sophomore pitchers: Jeff Niemann, Wade Townsend, and Philip Humber. Rice won its first three games in the tournament– a 4–2 win over Southwest Missouri State (now Missouri State University), a 12–2 defeat of defending champion Texas, and a second victory over Texas to advance to the championship round. Texas had already lost to Rice 2–1 earlier in the season. The Owls defeated Texas on catcher Justin Ruchti's one-run RBI single in the bottom of the 9th off of Texas closer Huston Street. The Owls' two wins against Texas was a change of outcome from the previous CWS, where Texas had beaten Rice in their opening game.

In the best-of-three championship series, Rice played against Stanford. Rice won the first game with its second consecutive walk-off victory, as Chris Kolkhorst scored from second on a throwing error in the bottom of the 10th to win 4-3. Stanford rallied in the second game the next night to win 8-3, but the Owls defeated the Cardinal in the final game 14–2 to win Rice's first national championship in a team sport. Each member of the Owls pitching rotation pitched in the championship series; Niemann recovered from three early runs to pitch seven scoreless innings in game one, Townsend pitched well in game two despite two seventh inning errors, and Humber threw a complete-game five-hitter to win game three.

In Houston after the championship series, the Owls were honored in a parade by the City of Houston. The University commissioned a painting of the championship to sell to fans and alumni that is still available in print form. The team also visited the White House, where then-President George W. Bush recalled watching Rice games in his youth and commended the team for their accomplishments.