Etherton was drafted by the Anaheim Angels in the 1st round of the 1998 MLB Draft. He made his major league debut on May 26, 2000 for the Angels against the Kansas City Royals. He started the game and pitched five innings while giving up three runs. He recorded his first win on June 13, 2000 against the Tampa Bay Devil Rays. He was 5-1 for the Angels in 11 starts in 2000 with a 5.52 ERA.
On December 10, 2000 he was traded by the Angels to the Cincinnati Reds for shortstop Wilmy Caceras. He missed all of the 2001 season and most of the 2002 season because of shoulder surgery and then made seven starts for the Reds in 2003. He was 2-4 with a 6.90 ERA in those appearances. He spent the entire 2004 season in the minor leagues with the AAA Louisville Bats.
Etherton signed as a minor league free agent with the Oakland Athletics for the 2005 season. He spent most of the season with the AAA Sacramento River Cats but made three starts for the Athletics when Rich Harden was injured in May. He was 1-1 with a 6.63 ERA in those starts.
He was signed as a minor league free agent by the Kansas City Royals in November 2005 and then selected in the minor league portion of the Rule V Draft by the San Diego Padres. The Padres traded him back to the Royals on May 26, 2006 for cash. He was 1-1 with a 9.39 ERA in 2 starts with the Royals while spending most of the season with the AAA Omaha Royals.