Perkins played his college ball for the Minnesota Golden Gophers in 2003 and 2004. With the Gophers in 2003, he went 10–2 and posted a 2.91 ERA with 117 strikeouts. In his 2004 season with the Gophers, he went 9–3 and posted a 2.83 ERA with 113 strikeouts. Perkins was drafted by the Minnesota Twins in the 1st round of the 2004 Major League Baseball draft, being picked 22nd overall.

Between the years of 2004–2008, Perkins played most of his games for the Minnesota Twins minor league system. He pitched for the Elizabethton Twins, Quad City Swing, Fort Myers Miracle, Gulf Coast Twins, New Britain Rock Cats, and the AAA Rochester Red Wings. In his three seasons with Minnesota Twins minor league teams, he pitched 386.2 innings, posting a 16–22 record with a 3.50 ERA and 380 strikeouts. He was ranked number 66 in Baseball America's Top 100 Prospects.

Perkins made his MLB debut on September 21, 2006, against the Boston Red Sox. Coming in to relieve teammate Matt Guerrier, Perkins pitched 1.1 innings of perfect baseball. Perkins pitched in 4 regular season games in the 2006 season, all in September as a relief pitcher. He pitched 5.2 innings giving up no runs and striking out 6.

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