Loup began 2012 with the Fisher Cats.
In the 2012 season, the Toronto Blue Jays used 32 different pitchers due to frequent injuries, and Loup was among these.
He was called up to replace Luis Pérez on July 14 after Pérez tore his ulnar collateral ligament.
In his debut, Loup retired all six batters he faced.

On August 3, Loup became the first pitcher in Blue Jays history to bat in an American League game, grounding out to begin the top of the 15th against the Oakland Athletics.
Loup closed out the season posting a 0-2 record with a 2.64 ERA and 21 strikeouts in 30​²⁄₃ innings.
The Toronto chapter of the Baseball Writers' Association of America (BBWAA) named him the Toronto Blue Jays 2012 Rookie of the Year that November.

Though he was considered one of the front-runners, there was still much competition for one of the limited 2013 bullpen spots as a relief pitcher.
His main competition was seen as Brett Cecil and J. A. Happ.
John Gibbons said, "How it best fits the team, how it all stacks up down there is really what it's going to come down to.
But we're going to go with the best guy, not because guys are out of options."
Reportedly, Loup learned that he had acquired one of the bullpen spots when Gibbons walked by his locker and said, "Oh, hey Loup—you made the team."

Loup pitched 1​¹⁄₃ innings of relief for the Blue Jays against the Cleveland Indians on Opening Day.
On April 10, in a game against the Detroit Tigers, Loup recorded his first career win.
On April 12, Loup recorded his first major league save in a game against the Kansas City Royals.
He would later record a second major league save in a game against the San Diego Padres on June 2.
On April 20, Loup committed a two-run throwing error in the eleventh inning against the New York Yankees.
During the first two months of the Blue Jays' lackluster 2013 season, Loup and other relief pitchers helped to keep the Blue Jays from more defeats.
Loup was the ninth and final pitcher in an eighteen-inning game against the Texas Rangers on June 8.
The game, which was the longest in Blue Jays history, resulted in a win after Loup gained a pair of groundouts.
In another game against the Rangers on June 14, Loup pitched in the eighth inning and participated in a shutout.
Loup ended the 2013 season with a 4–6 record, 2.47 ERA and 53 strikeouts in 69​¹⁄₃ innings.

Loup was one of eight pitchers in the bullpen for the Blue Jays' 2014 opening day.
On April 20, Loup walked three consecutive batters for the first time in his career, and took the loss as the Blue Jays fell to the Cleveland Indians 6–4.
On May 3, the Blue Jays announced that Loup would replace Sergio Santos as the team's closer until Casey Janssen returned from injury.
After walking as many batters in three months as he had the entire last season, Loup regained confidence after pitching the last few innings of a game on June 4 that went from a 3–2 lead to an 8–2 win against the Detroit Tigers.
Loup began 2012 with the Fisher Cats. In the 2012 season, the Toronto Blue Jays used 32 different pitchers due to frequent injuries, and Loup was among these. He was called up to replace Luis Pérez on July 14 after Pérez tore his ulnar collateral ligament. In his debut, Loup retired all six batters he faced.
On August 3, Loup became the first pitcher in Blue Jays history to bat in an American League game, grounding out to begin the top of the 15th against the Oakland Athletics. Loup closed out the season posting a 0-2 record with a 2.64 ERA and 21 strikeouts in 30​²⁄₃ innings. The Toronto chapter of the Baseball Writers' Association of America (BBWAA) named him the Toronto Blue Jays 2012 Rookie of the Year that November.
Though he was considered one of the front-runners, there was still much competition for one of the limited 2013 bullpen spots as a relief pitcher. His main competition was seen as Brett Cecil and J. A. Happ. John Gibbons said, "How it best fits the team, how it all stacks up down there is really what it's going to come down to. But we're going to go with the best guy, not because guys are out of options." Reportedly, Loup learned that he had acquired one of the bullpen spots when Gibbons walked by his locker and said, "Oh, hey Loup—you made the team."
Loup pitched 1​¹⁄₃ innings of relief for the Blue Jays against the Cleveland Indians on Opening Day. On April 10, in a game against the Detroit Tigers, Loup recorded his first career win. On April 12, Loup recorded his first major league save in a game against the Kansas City Royals. He would later record a second major league save in a game against the San Diego Padres on June 2. On April 20, Loup committed a two-run throwing error in the eleventh inning against the New York Yankees. During the first two months of the Blue Jays' lackluster 2013 season, Loup and other relief pitchers helped to keep the Blue Jays from more defeats. Loup was the ninth and final pitcher in an eighteen-inning game against the Texas Rangers on June 8. The game, which was the longest in Blue Jays history, resulted in a win after Loup gained a pair of groundouts. In another game against the Rangers on June 14, Loup pitched in the eighth inning and participated in a shutout. Loup ended the 2013 season with a 4–6 record, 2.47 ERA and 53 strikeouts in 69​¹⁄₃ innings.
Loup was one of eight pitchers in the bullpen for the Blue Jays' 2014 opening day. On April 20, Loup walked three consecutive batters for the first time in his career, and took the loss as the Blue Jays fell to the Cleveland Indians 6–4. On May 3, the Blue Jays announced that Loup would replace Sergio Santos as the team's closer until Casey Janssen returned from injury. After walking as many batters in three months as he had the entire last season, Loup regained confidence after pitching the last few innings of a game on June 4 that went from a 3–2 lead to an 8–2 win against the Detroit Tigers.
Aaron Loup