On August 9, 2003, Schlossnagle was named the head coach at TCU, whose baseball program had just completed its first year in the brand-new Lupton Stadium.

During his first season in Fort Worth, 2004, he led the Horned Frogs to a then-school record 39 wins and a Conference USA Tournament championship, clinching their first NCAA bid since 1994.

In 2005 and 2006, the Horned Frogs won their second and third consecutive conference tournament championships (2006 was in the Mountain West), which went along with two more NCAA Regional appearances.

In the postgame press conference following the Aggies' loss in game 3, Schlossnagle angrily berated a reporter for inquiring about a rumor that he had accepted the head coach position at rival Texas.

Despite this outburst during the press conference, Schlossnagle departed for rival Texas the following day on June 25, 2024, taking his entire coaching staff with him and attempting to persuade the players to transfer to the Longhorns.

"[2] On June 25, 2024, Schlossnagle was named the head baseball coach of the Texas Longhorns the day following the Aggies' loss in the College World Series finals.

So write that.” The move was widely criticized by numerous media outlets including ESPN, Houston Chronicle, FoxSports, CBS Sports, and others.

Several news outlets also reported that many in the Texas Baseball program knew about the deal prior to the 2024 College World Series as talks between Schlossnagle and Texas athletic director Chris Del Conte reportedly began in late April, over a month before the Longhorns even fired their own coach David Pierce,[4] though Schlossnagle denied there were any prior communications.