After his playing career ended, Slowey joined the Major League Baseball Players Association as an assistant.

Slowey drew little attention from Division I schools and ended up attending Winthrop University on an academic scholarship after scoring a 1420 on his SAT.

He went on to be named as a third-team All-American by Baseball America in 2005 when he had 14–2 record with 126 strikeouts, only 13 walks issued, and a 2.16 ERA.

Slowey ascended rapidly through the Twins minor league system and after failing to make the team as a dark horse candidate out of spring training, he began the 2007 season with the Triple-A Rochester Red Wings.

A highlight of the start occurred early in the game when in the first inning, Slowey showed excellent poise in working out of a bases loaded jam.

On July 5, 2007, after giving up five earned runs in 32⁄3 innings against the New York Yankees, Slowey was optioned back to the Triple-A Rochester Red Wings, exchanging his roster spot with Carmen Cali.

[6][7] Slowey pitched 232⁄3 innings for the Minnesota Twins in spring training, posting a 3–2 record and 4.94 ERA, earning him a spot on the starting rotation.

[17] On July 1, 2010, he left a game against the Detroit Tigers after he was hit in the ankle by a batted ball, but did not miss any time on the mound.

[19] On August 15, 2010, he pitched seven no-hit innings against the Oakland Athletics before being removed in the top of the eighth for Jon Rauch.

I'd be booing too because I want to see a no-hitter, but I also know I'm responsible for this guy's arm", as he alluded to the elbow tendinitis that caused Slowey to miss his last start.

[26] He was optioned to the Triple-A Columbus Clippers and subsequently spent the entire season on the minor-league disabled list.

[28] On January 15, 2013, Slowey signed a minor league deal with the Miami Marlins as a non-roster invitee with an invitation to spring training.

[34] After Tom Koehler was optioned and Ricky Nolasco was traded, Slowey got the start on July 8 against the Braves, pitching five scoreless innings.

[41] On December 22, 2014, Slowey signed a minor league contract with the Philadelphia Phillies that included an invitation to spring training.

He has taken a position in the Major League Baseball Player's Association as a special assistant to Tony Clark, the executive director.