He was drafted in the seventh round (199th overall) of the 1996 MLB Draft by the Kansas City Royals. Mullen played college baseball at The Citadel, The Military College of South Carolina and Dallas Baptist University. He spent five seasons in the Royals' minor league system before making his Major League debut in 2000 and spent parts of the next three seasons with the Royals before he was traded to the Los Angeles Dodgers in 2003 (with Victor Rodriguez) for Gookie Dawkins. He pitched primarily for the Dodgers minor league team in 2003, but spent part of the year in the majors.