In Stiffler's first season as an assistant, the Rams would boast one of their strongest campaigns in program history, winning 27 games and the 2007 CAA tournament.

On April 11, 2012, Stiffler was named the head coach on an interim basis when Paul Keyes stepped down to health reasons.

[5] Stiffler finished the 2012 season out with a 12–9 record, and in December 2012 was promoted to head coach on a full-time basis.

The Rams finished 40–25 overall with Stiffler leading the team to their first NCAA Division I Super Regional appearance, being recognized by both the NCBWA and Collegiate Baseball Coach of the Year.

[7] On July 12, 2022, it was reported that Shawn Stiffler is being hired to be the next head baseball coach at the University of Notre Dame.