Pebley's teams were 46-20 overall and 26-8 in the Mountain West Conference. Fresno State lost in the first round of the tournament both years.
She replaces Jeff Mittie, who left for Kansas State after a 15-year stint at TCU that included nine NCAA tournaments for a once-moribund program.
Before going to Fresno State, Pebley spent nine years at Utah State when the program was restarted in 2003 following a 25-year hiatus.
TCU struggled with the move from the Mountain West to the Big 12 in 2012-13, going 2-16 in conference. But the Horned Frogs improved to 8-10 this season.