He pitched for two seasons in various levels of the Toronto Blue Jays' minor league organization before his debut in 2006 as a starting pitcher.

Janssen was moved to the bullpen as a middle reliever and spot starter from 2007 to 2011, and in 2012 he was put in the closing role.

[1] At Fountain Valley, Janssen was a three-year letter winner, and set single-season records at the school for home runs (12), RBIs (44), and triples (5).

[3] In his first season, Janssen pitched as a fourth starter and long reliever, and held a record of 2–3 with a 5.57 ERA, but excelled in relief appearances, and also went 2–9 with a home run as a pinch hitter.

During his junior season, Janssen went 6–6 with a 5.88 ERA and 73 strikeouts, while also making appearances at first base and as a designated hitter.

[4] The Toronto Blue Jays selected Janssen out of UCLA in the fourth round of the 2004 draft.

[5] He made his professional debut for the Low-A Auburn Doubledays, posting a 3-1 record and 3.48 ERA in 10 games.

[6] When an injury to A. J. Burnett created an opening in the Blue Jays' rotation, Janssen was promoted from Syracuse and made his major-league debut against the Baltimore Orioles on April 27, 2006.

[9] Janssen was voted by the Baseball Writers' Association of America (BBWAA) as the top Blue Jays pitcher of 2012, narrowly edging out Brandon Morrow.

[10] On February 5, 2013, manager John Gibbons said that, barring injury, Janssen would have the closer role for the start of the 2013 regular season, over teammate Sergio Santos.

[19] On February 20, 2016, Janssen signed a minor league contract with the San Diego Padres that included an invitation to spring training.

[21] On June 16, 2016, Janssen signed a minor league contract with the Boston Red Sox.

[22] Janssen recorded a 2.87 ERA in 14 appearances between the Triple-A Pawtucket Red Sox and the Low-A Lowell Spinners before he opted out of his contract and was released on August 7.