Mahomes made his major league debut with the Twins in 1992. He made the team out of spring training, and started the sixth game of the season on April 12 against the Texas Rangers, pitching six innings and getting a no decision. He notched his first major league win in his next start on April 21 against the Seattle Mariners. Mahomes played with the Twins into the 1996 season, appearing in a total of 114 games during five seasons while compiling an 18–28 record with 5.82 ERA, with 217 strikeouts in innings. The Twins traded Mahomes to the Red Sox on August 26, 1996, in exchange for a player to be named later.
Boston Red Sox
Mahomes pitched a total of 21 games during the 1996 and 1997 seasons with Boston, registering a 6.85 ERA with 3–0 record and 11 strikeouts in innings. He was released by the Red Sox on June 27, 1997.
Yokohama BayStars
Mahomes played for the Yokohama BayStars of Nippon Pro Baseball, arriving with them midway through the 1997 season, and pitched for them through 1998.
Mahomes was signed by the Mets in December 1998. He went 8-0 in the 1999 season during 39 relief appearances, and helped the Mets reach the playoffs. Mahomes made four relief appearances during the postseason, recording a 2.25 ERA in eight innings pitched while striking out four, as the Mets lost to the Atlanta Braves in the NLCS. In 2000, Mahomes was 5–3 in 53 appearances, and while the Mets reached the 2000 World Series, Mahomes was left off the Mets' playoff roster. In his two seasons with the Mets, Mahomes appeared in 92 regular season games with a 4.74 ERA, 13–3 record, and 127 strikeouts in innings. He became a free agent in December 2000.
Texas Rangers
Mahomes signed with the Rangers in January 2001. During the 2001 season, he appeared in 56 games with a 5.70 ERA and 7–6 record, while striking out 61 in innings. Mahomes again became a free agent in November 2001.
Chicago Cubs
In January 2002, Mahomes signed with the Cubs. He made 16 appearances during the 2002 season, with a 3.86 ERA and 1–1 record, striking out 23 in innings. Mahomes became a free agent in October 2002.
Pittsburgh Pirates
Mahomes was signed by Pittsburgh in January 2003. He made nine appearances with the Pirates during the 2003 season, recording an 0–1 record with 4.84 ERA and 13 strikeouts in innings. This would prove to be his final season playing in MLB. Mahomes again became a free agent in September 2003. Overall, Mahomes pitched 11 seasons in MLB, making a total of 308 regular season appearances with a 42–39 record, 5.47 ERA, and 452 strikeouts in 709 innings pitched. He had 43 at bats during his career, with 11 hits and four RBIs.
Minor league journeyman
In, Mahomes pitched primarily for the Pittsburgh Pirates AAA affiliate, the Nashville Sounds, while appearing in nine games for the Pirates. In, he split the season between three organizations, pitching for the Edmonton Trappers in the Montreal Expos farm system, the Albuquerque Isotopes in the Florida Marlins system, and then again at Nashville at the end of the season. After spending with the Las Vegas 51s in the Los Angeles Dodgers organization, Mahomes turned to the independent leagues, starting with the Long Island Ducks of the Atlantic League. After going 11-4 with a 3.87 ERA, he signed with Kansas City Royals in August, but was released a month later. Mahomes began the 2007 season with the Sioux Falls Canaries of the American Association. On August 24, the Toronto Blue Jays signed him, and he appeared in three games for the Syracuse Chiefs before becoming a free agent at the end of the season. Mahomes signed with the Southern Maryland Blue Crabs of the Atlantic League in, but only appeared in two games for them before returning to Sioux Falls. He split the 2009 season between Sioux Falls and Grand Prairie.