His MLB debut was July 24, 1999, and, although a starter for most of his career up until this point, made three relief appearances, and then was traded to the Chicago Cubs, along with Ruben Quevedo and a minor league player to be named later (Joey Nation), for Terry Mulholland and José Hernández.

Bowie pitched well in relief for the Nationals' Triple-A affiliate New Orleans Zephyrs, and in July was called up to the majors.

He was effective as a set-up man in 15 relief appearances, posting an ERA of 1.37 before going on the disabled list and eventually missing the rest of the season.

On December 21, 2007, the Colorado Rockies signed Bowie to a minor league contract with an invitation to spring training.

[3] Bowie developed back problems during his playing career and rather than undergo disk fusion surgery that might need to be repeated, elected in August 2016 to have a spinal-cord stimulator implanted to suppress pain.

[3] After continuing breathing problems,[4] the Mayo Clinic found his lungs had electrical burns;[2] in May 2019 the device was removed at Barnes-Jewish Hospital in St. Louis, Missouri, by the same doctor who had repaired his groin injury in 2007.