Wells was Selected by the San Diego Padres in the 31st round of the 2002 Major League Baseball Draft, signed by San Diego Padres scout Jay Darnell in. That year, Wells was assigned to the Short-Season A Eugene Emeralds. He had a record of 4-6 with a 2.75 ERA. The ERA was good enough for seventh lowest among Northwest League starters. In Wells was sent up to the Single-A Fort Wayne Wizards. He compiled a 4-6 record with 4.09 ERA in 14 starts. This soon earned him a promotion to the Advanced-A Lake Elsinore Storm there he had a record of 4-6 with a 4.52 ERA in 12 starts. The Padres decided to keep Wells at the Advanced-A level but he soon found himself a promotion to the Double-A Mobile BayBears in. He went 13-8 with a 3.68 ERA in a combined 163 innings between the two clubs, tied for the lead among Padres' farmhands in wins, while his ERA ranked fourth. Wells captured the California League ERA title and was named the league's Pitcher of the Year. Wells was named the Padres Minor League Pitcher of the Year at the club's annual organization postseason Awards Dinner on November 3. Wells split the season between Double-A Mobile and the Triple-A Portland Beavers, Wells combined record was 6-12 with a 5.16 ERA in 27 starts. In 12 games at Mobile, went 4-3 with a 2.64 ERA. Wells was promoted to Triple-A on June 17 where he struggled with a 2-9 record with a 7.27 ERA. In Wells saw consistent action at the Triple-A level with Portland but struggled in his transition to the bullpen. Wells went 2-9 with a 5.24 ERA. He also recorded nine saves. was again a disappointing season for Wells, he had a 1-1 record with a 5.85 ERA. Even though his performance was sub-par, he was called up for the first time in his career on May 22,, and made his major league debut with the Padres on May 24.
Seattle Mariners
After just one more appearance with the Padres, he was traded to the Mariners on May 28 for Cha Seung Baek and was assigned to Triple-A Tacoma Rainiers. He was called up by the Mariners on July 10, but optioned to the Rainiers when Félix Hernández was activated the next day. Wells pitched for the Tacoma Rainiers after starting the season with the Double-A West Tenn Diamond Jaxx in.
